Error Locating Program Bowtie
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faq • rss Community Log In Sign Up Add New Post Question: How do I run Tophat? 1 18 months ago by amnoronha1016 • 10 United States amnoronha1016 • 10 wrote: I am using the following command: ./tophat2 tophat paired end example -r 210 -p 8 -G ~/Data/*.gtf ~/Data/hg19f/hg19 ~/Data/thyroid1,~/Data/testes1 ~/Data/thyroid2,~/Data/testes2 but I'm getting the error: [2015-04-11 tophat2 example 21:58:47] Checking for reference FASTA file Warning: Could not find FASTA file /home/anoronh4/HW3/hg19f/hg19.fa [2015-04-11 21:58:47] Reconstituting reference FASTA file from Bowtie tophat command line index Error locating program: bowtie-inspect The files in hg19f are: hg19.1.ebwt hg19.3.ebwt hg19.rev.1.ebwt make_hg19.sh hg19.2.ebwt hg19.4.ebwt hg19.rev.2.ebwt Since when do I need a .fa file? bowtie tophat • 3.0k views ADD COMMENT • link • Not tophat2 tutorial following Follow via messages Follow via email Do not follow modified 18 months ago • written 18 months ago by amnoronha1016 • 10 1 one correction: ./tophat2 -r 210 -p 8 -G ~/Data/*.gtf ~/Data/hg19f/hg19 ~/Data/thyroid1,~/Data/testes1 ~/Data/thyroid2,~/Data/testes2 Give full names of fasta/q files. Why its *.gtf ? ADD REPLY • link written 18 months ago by Goutham Atla ♦ 6.1k 1 Is bowtie2 installed? Is bowtie-inspect in the path? ADD REPLY • link written 18
Tophat Tutorial
months ago by Sean Davis ♦ 22k 1 18 months ago by Mehmet • 100 Japan Mehmet • 100 wrote: Hi, I think you want to align RNAseq reads to your reference genomes. If so, and If you have paired-end reads of RNAseq (R1 and R2), you should follow these steps: 1. Build index files using bowtie2 (bowtie2 is for tophat2) using "bowtie2-build your fasta file" After generating bowtie index files, do not comprise them. just leave in your directory. in your case "The files in hg19f are:" you put all bowtie index files in a file and used the file in your tophat command. you should not do this. first, you will need to use your fast file to make bowtie index file, you will use your the same genome file in tophat command, not index files. 2. Run tophat command. in tophat command, you need to use your fasta (genome file) and RNAseq files (R1 and R2). The fast file is in .fa format. Ransom files are generally in .gz (gunzip) format. here is a sample tophat command: tophat -o OUT.dir2 --library-type fr-secondstrand --mate-std-dev 50 -a 6 --microexon-search --min-segment-intron 10 --max-segment-intron 20000 -i 30 -I 20000 -r 0 genome.fa R1.fastq.gz R2.fastq.gz ADD COMMENT • link written 18 months ago by Mehmet • 100 1 18 months ago by Parham &bu
• rss Community Log In Sign Up Add New Post Question: Tophat 0 5.2 years ago by Luciano Cosme •
Tophat2 Download
220 Luciano Cosme • 220 wrote: Hi, I am running galaxy locally bowtie2 index and when I perform alignments with TopHat I get the following error: Error in tophat: [Fri Jul bowtie index 29 17:55:47 2011] Beginning TopHat run (v1.3.1) [Fri Jul 29 17:55:47 2011] Preparing output location ./tophat_out/ [Fri Jul 29 17:55:47 2011] Checking for Bowtie index files [Fri Jul https://www.biostars.org/p/137875/ 29 17:55:47 2011] Checking for reference FASTA file Warning: Could not find FASTA file /tmp/tmp1dXHLG/dataset_26.dat.fa [Fri Jul 29 17:55:47 2011] Reconstituting reference FASTA file from Bowtie index Executing: /bin/bowtie-inspect /tmp/tmp1dXHLG/dataset_26.dat > ./tophat_out/tmp/dataset_26.dat.fa [Fri Jul 29 17:56:39 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Fri Jul 29 17:56:39 2011] Checking for Samtools Error locating program: samtools I installed the https://biostar.usegalaxy.org/p/2966/ samtools (in several places already), but it seems I did not put it in the right place. So where galaxy search for it? Thank you. Luciano alignment bowtie samtools bam • 740 views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 5.2 years ago by Jennifer Hillman Jackson ♦ 20k • written 5.2 years ago by Luciano Cosme • 220 0 5.2 years ago by Jennifer Hillman Jackson ♦ 20k United States Jennifer Hillman Jackson ♦ 20k wrote: Hello Luciano, Here are is the core wiki link to help with NGS tools (including SamTools) set up and installation. http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup For next time, the galaxy-dev@bx.psu.edu mailing list would be the best place to send new questions or even follow-up questions to this one if problems persist. The development community can be very helpful in sorting out local installation issue that may come up. Subscribing may also be of interest: http://lists.bx.psu.edu/listinfo/galaxy-dev http://galaxyproject.org/Support Thanks! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ADD CO
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