tophat2 stuck on "generating sam header"
Hello, I have just installed tophat2 on linux along with bowtie, and I am trying to run it on some mRNA data. I installed the index for hg19 from the bowtie2 website, and ran the make_hg19.sh script. After this, I ran tophat once on my index and it looks like it compiled hg19 into one hg19.fa file since my fasta was split into the chromosome files. After running my tophat with hg 19 as the index it keeps getting stuck on generating sam header. I dont have samtools installed, but I have the new version of tophat (10/2/14) which says it comes with samtools installed.
I run:
tophat2 /bowtie/index/hg19 ex_001.fastq, ex_002.fastq, ex_003.fastq, ex_004.fastq
and I get the following message to my terminal where it gets stuck:
[2014-10-05 23:28:54] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2014-10-05 23:28:54] Checking for Bowtie
Bowtie version: 2.2.3.0
[2014-10-05 23:28:54] Checking for Bowtie index files (genome)..
[2014-10-05 23:28:54] Checking for reference FASTA file
[2014-10-05 23:28:54] Generating SAM header for ../../tools/bowtie/index/hg19
Please advise
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crrobles2 •
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This step takes a little while - how long did you leave it running for?
why are you mapping many fastq files in one run?
My understanding was that you could map many reads in one run with tophat.
I note that your command line example has a spaces around the commas - that would not be correct but may just be a mistype on this site
I only have spacing after the commas. Could this possibly have to do with the new build of tophat released on 10/2/14? This release includes samtools. I am thinking about trying to do it with an older version.
Read the manual and make sure you have the command right. The spaces, commas and file order matter as they separate read pairs and allow for mixed type input. http://ccb.jhu.edu/software/tophat/manual.shtml
I've successfully used this version (TopHat 2.0.13 release 10/2/2014).
Does Bowtie alone works with this index ?
yes, It was my understanding too, I also couldn't figure out why it failed so I ran them all seperately
In your case, its getting out while making SAM headers, which means there should be some issue with your bowtie index or I am not sure