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Old 09-11-2013, 05:41 PM   #1
kumtl
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Question Tophat different outputs according to the different number of threads

Hi! All,

I don't know anyone who had the same issue like I had, while using tophat software. I have a server which has 16 cores.

I tried to run tophat with different thread number for one of my sample. Unfortunately I had different outputs. (single-end RNA-seq data)

1. tophat -p 16 --no-coverage-search --solexa-quals --keep-tmp --b2-very-sensitive -G Gene_GTF --no-novel-juncs -o Tophat_out bowtie_index 1st_sample.fastq

2. tophat -p 4 --no-coverage-search --solexa-quals --keep-tmp --b2-very-sensitive -G Gene_GTF --no-novel-juncs -o Tophat_out bowtie_index 1st_sample.fastq

Any idea?
Thanks in advance...
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Old 09-11-2013, 11:25 PM   #2
simonandrews
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When you say you got different outputs do you mean that you got the same hits, but in a different order (which wouldn't be surprising), or that you got different hits (which would)?
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Old 09-11-2013, 11:33 PM   #3
kumtl
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simonandrews, thanks for your inquiry

Of course, I know about different order of outputs.
In my case, the result hits were different. Simply, the read numbers in accepted_hits.bam and unmapped.bam were slightly different. (-p 4 vs -p 16)

I don't know why this problem was happened. I tried the other number of threads (like, 1, 2, and 4) and their results were all same, except 16 (max num of available threads).

--Kumtl
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Old 09-11-2013, 11:39 PM   #4
simonandrews
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If this is reproducible then I think it's one to send to the tophat authors.
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Old 09-11-2013, 11:46 PM   #5
kumtl
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That's not bad idea. I'll let them know, if this problem happened again.
Thanks
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Old 09-12-2013, 12:53 AM   #6
kumtl
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Simon, I have another question about tophat.

As you know from my post, I had different outputs because of different number of threads.
So, I tried to remap reads from unmapped.bam, and I got another hits from them. Of course, I applied exactly same option on tophat command line.

Do you have any idea?
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