A text file in the required format can be generated using the extractsplicesites () function, starting from an annotation file in gtf or gff3 format, or from a GRanges or TxDb object. RNA-seq7- Hisat2 . Problem solved Except, that is not at all how you solve that problem. ht2 etc. ht2" for example. Also, the htseq-count literature states that UCSC encoded gtf files do not work with htseq because "the geneid. Share Improve this answer. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. HISAT2 tries to extend seeds to full-length alignments. Based on an extension of BWT for graphs (Sir&233;n et al. Log In My Account kc. start Start position of the feature (exon, transcript, etc), using a 1-based index. Quesiton Is anyone else getting "Could Not Locate Game Executable Entry in the catalogue (aces. For example. You can change your preferences at any time by returning to this site or visit our sh. 2 5. I have redownloaded the index files (Drosophila) and also redownloaded hisat2. The basename is the name of any of the index files up to but not including the final. We want to use 8 threads rsem-calculate-expression -p 8 &92; --no-qualities &92; datammliver. A text file in the required format can be generated using the extractsplicesites () function, starting from an annotation file in gtf or gff3 format, or from a GRanges or TxDb object. I am trying to run Hisat2 on FASTA files. Feb 03, 2015 Could not locate a Bowtie index corresponding to basename, The SAMBAM file declares less than one. -1 <m1>. log" threads 2 wrapper "v1. make USESRA1 NCBINGSDIRpathtoNCBI-NGS-directory NCBIVDBDIRpathtoNCBI-NGS-directory , where NCBINGSDIR and NCBIVDBDIR will be used in Makefile for -I and -L compilation options. The basename is the name of any of the index files up to but not including the final. Dec 01, 2015 when I am doing initial bowtie run, the error shows Could not locate a Bowtie index corresponding to basename "Triticumaestivum. It indicates, "Click to perform a search". Zeynep the error is Could not locate a HISAT2 index corresponding to basename referenceshisat2indexmmu. The basename is the name of any of the index files up to but not including the final. Dec 29, 2021 The problem is probably that the tar process creates a folder with the genome files but the input for -x is not the folder with the index files but the basename of the index files itself. 7k views Read more here Source link. I have redownloaded the index files (Drosophila) and also redownloaded hisat2. Sep 27, 2019 Bowtie2Could not locate a Bowtie index corresponding to basename "homes45mouse" (base) s45HP45 bowtie2 -x homes45mouse SRR3151474. Note HISAT2 is not designed with large values for -k in mind, and when aligning reads to long, repetitive genomes, large -k could make alignment much slower. alignment software and mapping index, corresponding to the software should be specified by the user. Hisat has always worked for me and I&39;ve only just encountered this issue now. ht2 etc. Share Improve this answer. It seems that Hisat can&39;t read the index files, however I&39;m pretty sure its not due to typos. HISAT2 . Problem solved Except, that is not at all how you solve that problem. A magnifying glass. Could not locate a Bowtie index corresponding to basename "Triticumaestivum. From the Procedure part of the above article there are fifteen tasks, which I would like to do, but in the eights task I got stuck. Could not locate a Bowtie index corresponding to basename, The SAMBAM file declares less than one. samCould not locate a Bowtie index corresponding to basename "homes45mouse"Error Encountered internal Bowtie 2. dictlist dataa. Also, the htseq-count literature states that UCSC encoded gtf files do not work with htseq because "the geneid. If you have, say, three reference sequences named 1. ht2 etc. The structure declaration is followed by an. Jul 07, 2018 HISAT2 (STARTopHatHISAT2PESE readreadSTAR HISAT2STARTopHat22. 0 on my MacOS Mojave 10. We and our partners store andor access information on a device, such as cookies and process personal data, such as unique identifiers and standard information sent by a device for personalised ads and content, ad and content measurement, and audience insights, as well as to develop and improve products. RNAseq(4)-Hisat2Samtools RNA-seq(5)Hisat2 hisat2reads hisat2 1. YKY Junior Member. Hisat has always worked for me and I&39;ve only just encountered this issue now. fasta> This will create new files with the provided basename and extensions . gz md5sum. source activate wes conda bowtie2-build hg38. Feb 03, 2015 Could not locate a Bowtie index corresponding to basename, The SAMBAM file declares less than one. I&39;m running Hisat2-2. There is also a script in the folder called "makegrcm38. ht2 etc. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. 0 on my MacOS Mojave 10. sam Could not locate a Bowtie index corresponding to basename "homes45mouse" Error Encountered internal Bowtie 2 exception. A magnifying glass. ht2 etc. 8 years ago Hannah Dixon 0 Hi, I am trying to run Hisat2 on FASTA files. The thing to do is either restore the names back to the original or download a new copy and use hg18 as "basename" for the index. Hi all, I used the hisat2 index builder data manager to create a hisat2 reference for a local ga. ht2 where n is a number from 1 to 8 in the working directory (ls command). Share Improve this answer. I have been attempting to map reads to a reference genome using HISAT2 using the Pertea, et al 2016 Nature Protocols paper. Since it&39;s likely not set to anything, it&39;s just ignored. It indicates, "Click to perform a search". In order to address that I was asking that you run the command in my comment and show us the output. ht2 genome. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. bug external Reported by someone else. Hello everyone I am first time trying to use HISAT, I am getting the following error message. Related Topics. I&x27;m running Hisat2-2. Where can I find HISTAT2INDEXES-x <hisat2-idx> The basename of the index for the reference genome. Where can I find HISTAT2INDEXES-x <hisat2-idx> The basename of the index for the reference genome. I&39;m running Hisat2-2. It seems that Hisat can't read the index files, however I'm pretty. . After long step of HISAT2 index building you will see 8 files refer. However, the output for our problem files following completion of the HISAT is gzip inputr. This tool is. fa hg38 & > nohup01. ht2 etc. Then in order to run htseq-count I downloaded grcm38 gtf file from Ensembl. By using -x mntmiczfstidebowtie2-indexhg19, you're telling bowtie2 that you have files like mntmiczfstidebowtie2-indexhg19. Dec 29, 2021 Dec 30, 2021 at 1138 Add a comment 1 Answer Sorted by 0 The problem is probably that the tar process creates a folder with the genome files but the input for -x is not the folder with the index files but the basename of the index files itself. Changing to directory the index is located and running bowtie2. , Thornton, M. linux - Bowtie. For example. Could not locate a Bowtie index corresponding to basename, The SAMBAM file declares less than one. Could not locate a hisat2 index corresponding to basename. It indicates, "Click to perform a search". Log In My Account kc. I'm working with mouse data, trying to align to mm9, not a custom genome. genome Can anyone offer help on this Thanks much, Enzo Enzo - 2015-12-01. Based on an extension of BWT for graphs (Sirn et al. I am able to successfully generate an index (using the hisat2-build comma. 0 on my MacOS Mojave 10. HISAT2 . We present a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index. Based on an extension of BWT for graphs (Sirn et al. Jan 17, 2018 Changing to directory the index is located and running bowtie2. By using -x mntmiczfstidebowtie2-indexhg19, you're telling bowtie2 that you have files like mntmiczfstidebowtie2-indexhg19. However, I did use bowtie2-build to construct this library, and the bowtie2 command itself recognizes the basename properly (see the third example below) while the bowtie2-align command has the same issue that TopHat did (see the second example below). 820 views. 2014, we designed and implemented a graph FM index (GFM), an original approach. ADD COMMENT link 5. I&39;m running Hisat2-2. You don't specify a folder,. Could you clarify the state of your local for both ADD REPLY link written 22 months ago by Jennifer Hillman Jackson 25k. append (data) listdictlist dictdatalist. Create("Default")) if just embedded SI varhost . I am able to successfully generate an index (using the hisat2-build comma. I&39;m running Hisat2-2. After creating the index, reads can be aligned using the hisat2 wrapper function. , Thornton, M. gz not in gzip format Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of &39;int&39; (ERR) hisat2-align died with signal 6 (ABRT) (core dumped). It seems that Hisat can&39;t read the index files, however I&39;m pretty sure its not due to typos. 2 bowtie2. Set the Time filter field name to timestamp. All with the same result. -1 <m1>. ht2 etc. Hisat has always worked for me and I've only just encountered this issue now. HISAT2 . It indicates, "Click to perform a search". ht2 etc. Hisat has always worked for me and I&39;ve only just encountered this issue now. It seems that Hisat can&39;t read the index files, however I&39;m pretty sure its not due to typos. ht2 genome. Nov 21, 2022, 252 PM UTC an ob ww lg. esc "i" esc ex . May 25, 2017 50bp contig n 40bp contig HISAT2 RNA-seq . YKY Junior Member. The basename is the name of any of the index files up to but not including the final. 1 years ago GenoMax 122k You are likely missing a leading in path for index name usrbinrn6genome in your command. Web. Dec 29, 2021 The problem is probably that the tar process creates a folder with the genome files but the input for -x is not the folder with the index files but the basename of the index files itself. It indicates, "Click to perform a search". wz; gm. Default 5 (linear index) or 10 (graph index). I&39;m using the following script centrifuge-build -p 8 --conversion-table seqid2taxid. Also, the htseq-count literature states that UCSC encoded gtf files do not work with htseq because "the geneid. dmp inputsseqbac. The basename is the name of any of the index files up to but not including the final. The basename is the name of any of the index files up to but not including the final. - Type "servies" into Cortana search window and click "Services (desktop app)" - Search for "Apple OS Switch Manager" in the name column and right click on it, select &39;properties&39;. Could not locate a hisat2 index corresponding to basename yd xz. You see, the messages you are getting come from UEFINTFS which is a chain loader that attempts to load a NTFS driver, and then execute the UEFI bootloader on the NTFS partition, if there exists one. It seems that Hisat can&39;t read the index files, however I&39;m pretty sure its not due to typos. You probably meant -x mntmiczfstidebowtie2-indexhg19hg19 or something like that. It indicates, "Click to perform a search". Steps for fix - Boot W10. bz Fiction Writing. After that the Mac will boot into the Mac OS X partition. ht2 etc. The following are my command lines. I am newbie to linux and NGS. ss -p 6 hg19. RNAseq(4)-Hisat2Samtools RNA-seq(5)Hisat2 hisat2reads hisat2 1. Share Improve this answer Follow answered Dec 30, 2021 at 1213 user3051 Add a comment Your Answer. HISAT2 does not find alignments in any specific order, so for reads that have more than N distinct. nohup bowtie2-build hg38. The basename is the name of any of the index files up to but not including the final. It seems that Hisat can&x27;t read the index files, however I&x27;m pretty sure its not due to typos. and the output file name where the alignments should be written. I&39;m running Hisat2-2. Where can I find HISTAT2INDEXES -x <hisat2-idx> The basename of the index for the reference genome. In the desktop app, click Options and select Scan and Repair. genome" Command bowtie --wrapper basic-0 -c Triticumaestivum. hisat2looks for the specified indexfirst in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. Im trying to use HISAT2 but cannot get the job done this message is given "This is a new data. By using -x mntmiczfstidebowtie2-indexhg19, you're telling bowtie2 that you have files like mntmiczfstidebowtie2-indexhg19. It did not work. It indicates, "Click to perform a search". Your preferences will apply to this website only. For the support of SRA data access in HISAT2, please download and install the NCBI-NGS toolkit. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. HISAT2 RNA-seq . 50bp contig n 40bp contig . hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. The basename is the name of any of the index files up to but not including the final. hisat2looks for the specified indexfirst in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. The codes were as follows >library (Rsubread) >library (limma) >library (edgeR) >buildindex (basename "Homosapiens. When I run this script in that directory, it returns the error "Could not find hisat2-build in current directory or in PATH". Could not locate a Bowtie index corresponding to basename "largeidxlib" I am 99. , Park, C. gz md5sum. I am generating the HISAT2 index for mm9, which is in the drop-down menu of the Data Manager for generating HISAT2 indexes. RNA-Seq Hisat2 10k views. However, the output for our problem files following completion of the HISAT is gzip inputr. When running make, specify additional variables as follow. fa hg38 bowtie2 . hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. fa hg38 bowtie2 . The thing to do is either restore the names back to the original or download a new copy and. could not locate hisat2 index corresponding to basename homedesktopindex filesh19genome Thanks. A magnifying glass. That&x27;s what the &92;efi&92;boot&92;bootx64. ht2 etc. If the index files were originally named hg18 then you can't rename them to chr1. HISAT2 . Where can I find HISTAT2INDEXES-x <hisat2-idx> The basename of the index for the reference genome. instructions for fetching and install mm10 genome and hisat indexing for local galaxy Hi all, Is there a kind soul that could take me through a step-by-step of fetching and indexing. 1 years ago GenoMax 122k You are likely missing a leading in path for index name usrbinrn6genome in your command. ht2 genome. Then in order to run htseq-count I downloaded grcm38 gtf file from Ensembl. HISAT2 can incorporate exons and splice sites into the index file for alignment. I am trying to run Hisat2 on FASTA files. A text file in the required format can be generated using the extractsplicesites () function, starting from an annotation file in gtf or gff3 format, or from a GRanges or TxDb object. - Once set to automatic, below startup type click "start". samCould not locate a Bowtie index corresponding to basename "homes45mouse"Error Encountered internal Bowtie 2. Dec 29, 2021 The problem is probably that the tar process creates a folder with the genome files but the input for -x is not the folder with the index files but the basename of the index files itself. instructions for fetching and install mm10 genome and hisat indexing for local galaxy Hi all, Is there a kind soul that could take me through a step-by-step of fetching and indexing. Is this the memory requeriment also for the RefSeq database I&39;m trying to make it work but been unsuccesful in creating a bacterial index (199 (comment)). If the index files were originally named hg18 then you can&39;t rename them to chr1. You can either find a larger-memory machine or use other index. RNAseq(4)-Hisat2Samtools RNA-seq(5)Hisat2 hisat2reads hisat2 1. Web. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. Could not locate a Bowtie index corresponding to basename "largeidxlib" I am 99. HISAT2 tries to extend seeds to full-length alignments. If the pattern doesn&x27;t exist, create it manually. Last edited by GenoMax; 12-29-2014, 0549 AM. However, I did use bowtie2-build to construct this library, and the bowtie2 command itself recognizes the basename properly (see the third example below) while the bowtie2-align command has the same issue that TopHat did (see the second example below). The basename is the name of any of the index files up to but not including the final. From the Procedure part of the above article there are fifteen tasks, which I would like to do, but in the eights task I got stuck. Click the Options dropdown menu and select Show in Explorer. Fatal Errors occurring with htseq analysis. I&39;m running Hisat2-2. If you would like to install HISAT by copying the HISAT executable files to an existing directory in your PATH, make sure that you copy all the executables, including hisat, hisat-align-s, hisat-align-l, hisat-build, hisat-build-s, hisat-build-l, hisat-inspect, hisat-inspect-s and hisat-inspect-l. dmp --name-table taxonomynames. Hisat has always worked for me and I&39;ve only just encountered this issue now. For example ryanmaximus hisat2 ls bin convertChromosomesChain. Where can I find HISTAT2INDEXES-x <hisat2-idx> The basename of the index for the reference genome. For debugging. Any additional arguments to the hisat2-build binary. Also, the htseq-count literature states that UCSC encoded gtf files do not work with htseq because "the geneid. Adding the directory the index is located in to PATH. wz; gm. Open "Could not locate a Bowtie index corresponding to basename "refdirbarcodes-ref" 23. sam -U SRR404331ch4. fa genome nohup bowtie. I am generating the HISAT2 index for mm9, which is in the drop-down menu of the Data Manager for generating HISAT2 indexes. When I try running a small test data set with HISAT2, the job goes green and returns an empty file with the message "Could not open index file mntgalaxyIndicesmm9hisat2indexmm9mm9. 7k views Read more here Source link. fa hg38 & > nohup01. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). my stepchild is ruining my marriage, crilist
You probably meant -x mntmiczfstidebowtie2-indexhg19hg19 or something like that. . Could not locate a hisat2 index corresponding to basename
dmp --name-table taxonomynames. sam Could not locate a Bowtie index corresponding to basename "homes45mouse" Error Encountered internal Bowtie 2 exception. ht2 etc. fa hg38 bowtie2 . The basename is the name of any of the index files up to but not including the final. txt md5sum. How to Read Literature Like a Professor - MsEffie. I would like to include spliced alignment. gz md5sum. bowtie-build seems to think that your genome. fa" Error Encountered internal HISAT2 exception (1) Command usrlocalbinhisat2-align-s --wrapper basic-0 -x Slycopersicumchromosomes. Nov 21, 2022, 252 PM UTC an ob ww lg. That would mean that, if you have to map on reference number 2, you&x27;ll have to specify -x pathto2index. 0 on my MacOS Mojave 10. Web. dmp inputsseqbac. Web. 2014), we designed and implemented a graph FM index (GFM), an original approach and its first. Where can I find HISTAT2INDEXES -x <hisat2-idx> The basename is the name of any of the index files up to but not including the final. The basename of the index for the reference genome. HISAT2 comes with several index types Hierarchical FM index (HFM) for a reference genome (index base genome) Hierarchical Graph FM index (HGFM) for a reference genome plus SNPs (index base genomesnp) Hierarchical Graph FM index (HGFM) for a reference genome plus transcripts (index base genometran). 0 on my MacOS Mojave 10. Placed the index in a folder in the bowtie2 directory, in my downloads directory, and the desktop. ht2 etc. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. I have redownloaded the index files (Drosophila) and also redownloaded hisat2. The basename is the name of any of the index files up to but not including the final. Character scalar. -x <hisat2-idx> The basename of the index for the reference genome. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. The is just meant to show the end of the command prompt. bt2 that it should use. fa &92; refmouse125 &92; mmliversinglewithoutquals. 0 on my MacOS Mojave 10. 0 on my MacOS Mojave 10. I&39;m running Hisat2-2. A magnifying glass. Tour Start here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this site. Based on an extension of BWT for graphs (Sirn et al. Where can I find HISTAT2INDEXES -x <hisat2-idx> The basename of the index for the reference genome. Hi, I am trying to analyze RNAseq data with HISAT2. ht2" for example. 8 years ago Hannah Dixon 0 Hi, I am trying to run Hisat2 on FASTA files. HISAT2 does not find alignments in any specific order, so for reads that have more than N distinct. fastq (ERR) hisat2-align exited with value 1. Could not locate a HISAT2 index corresponding to basename "Slycopersicumchromosomes. Also, the htseq-count literature states that UCSC encoded gtf files do not work with htseq because "the geneid. The thing to do is either restore the names back to the original or download a new copy and use hg18 as "basename" for the index. HISAT2 . Where can I find HISTAT2INDEXES -x <hisat2-idx> The basename is the name of any of the index files up to but not including the final. When I run this script in that directory, it returns the error "Could not find hisat2-build in current directory or in PATH". May 07, 2020 RNA-seq (3) . ADD COMMENT link 5. It indicates, "Click to perform a search". Set the Time filter field name to timestamp. I am trying to run Hisat2 on FASTA files. fa Total time for call to driver() for forward index 000000 Error Encountered internal HISAT2 exception (1) Command hisat2-build --wrapper basic-0" the command and output of the terminal is as follows. From the Procedure part of the above article there are fifteen tasks, which I would like to do, but in the eights task I got stuck. instructions for fetching and install mm10 genome and hisat indexing for local galaxy Hi all, Is there a kind soul that could take me through a step-by-step of fetching and indexing. ht2 etc. Hi, I am trying to analyze RNAseq data with HISAT2. hisat2 HISAT2 HISAT2. Web. We introduce WSL to use bioinformatics tools for Linux systems on Windows. We want to use 8 threads rsem-calculate-expression -p 8 &92; --no-qualities &92; datammliver. 2 bowtie2. Where can I find HISTAT2INDEXES-x <hisat2-idx> The basename of the index for the reference genome. Could not locate a Bowtie index corresponding to basename "largeidxlib" I am 99. exon GENOME genometran Where "GENOME" contains a comma separated list of fasta files (one for each chromosome) I&39;m using the "buildindex. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. hisat2-build Error Encountered internal HISAT2 exception (1) hisat2. Could not locate a Bowtie index corresponding to basename "Triticumaestivum. The whole-genome index searching strategy (Fig. The Hisat2. YKY Junior Member. You probably meant -x mntmiczfstidebowtie2-indexhg19hg19 or something like that. sam Could not locate a Bowtie index corresponding to basename "homes45mouse" Error Encountered internal Bowtie 2 exception. Hisat has always worked for me and I&x27;ve only just encountered this issue now. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. Hi all, I used the hisat2 index builder data manager to create a hisat2 reference for a local ga. The basename is the name of any of the index files up to but not including the final. However, I did use bowtie2-build to construct this library, and the bowtie2 command itself recognizes the basename properly (see the third example below) while the bowtie2-align command has the same issue that TopHat did (see the second example below). source activate wes conda bowtie2-build hg38. Character scalar. In the case of a large index these suffixes will have a ht2l termination. The basename is the name of any of the index files up to but not including the final. ht2 etc. All with the same result. That&x27;s what the &92;efi&92;boot&92;bootx64. This is a perennial question, I guess the documentation isn&39;t explicit enough here. Could not locate a Bowtie index corresponding to basename "largeidxlib" I am 99. Could not locate a Bowtie index corresponding to basename "largeidxlib" I am 99. Open the Battle. -1 <m1>. 1 A, left) needs to search each mapping position one by one, which can be very time consuming. By default, this script builds and index for just the base files, since alignments to those sequences are the most useful. Share Improve this answer Follow answered Dec 30, 2021 at 1213 user3051 Add a comment Your Answer. Where can I find HISTAT2INDEXES -x <hisat2-idx> The basename is the name of any of the index files up to but not including the final. could not locate hisat2 index corresponding to basename homedesktopindex filesh19genome Thanks. - Type "servies" into Cortana search window and click "Services (desktop app)" - Search for "Apple OS Switch Manager" in the name column and right click on it, select &39;properties&39;. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2INDEXES environment variable. The basename is the name of any of the index files up to but not including the final. nohup bowtie2-build hg38. A magnifying glass. alignment software and mapping index, corresponding to the software should be specified by the user. hisat2 indexl" Error . Dec 29, 2021 Dec 30, 2021 at 1138 Add a comment 1 Answer Sorted by 0 The problem is probably that the tar process creates a folder with the genome files but the input for -x is not the folder with the index files but the basename of the index files itself. Oct 08, 2020 Have a question about this project Sign up for a free GitHub account to open an issue and contact its maintainers and the community. If you actually type hisat2, you&39;re not executing the hisat2 program, but whatever the hisat2 variable is set to. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. Web. 7k views Read more here Source link. Placed the index in a folder in the bowtie2 directory, in my downloads directory, and the desktop. All with the same result. Steps for fix - Boot W10. , Bennett, C. However, I did use bowtie2-build to construct this library, and the bowtie2 command itself recognizes the basename properly (see the third example below) while the bowtie2-align command has the same issue that TopHat did (see the second example below). The basename is the name of any of the index files up to but not including the final. After that the Mac will boot into the Mac OS X partition. There is also a script in the folder called "makegrcm38. Web. The basename is the name of any of the index files up to but not including the final. YKY Junior Member. end End position of the feature, using a 1-based index. Stack Exchange Network. . hoobs to homebridge