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Old 05-24-2012, 11:31 PM   #1
Location: Singapore

Join Date: May 2012
Posts: 48
Default Tophat - Should i keep unmapped_left.fq.z?


I am new to RNA-Seq and Tophat.
I am facing space issue with tophat, which has led me to think that I should delete files if they are "crap".

This particular file "unmapped_left.fq.z" is kinda huge(in space), can I get rid of it?What is the purpose of this file?

Thank you.

Best Regards,
wilson90 is offline   Reply With Quote
Old 05-25-2012, 12:49 AM   #2
Location: Turin, Italy

Join Date: Oct 2010
Posts: 66

That should be in the tmp file and tophat will delete it in the end of its run, at least that's what I've seen.
I don't know in which steps it needs that file, you could check in the source code to see if you can delete if even if it's already running.
EGrassi is offline   Reply With Quote
Old 05-27-2012, 12:15 AM   #3
Location: KSA

Join Date: Dec 2011
Posts: 37


I am also having this file at the end.... Dose it affect the created bam file or not? Can I proceed with my .bam file for further use?
AsoBioInfo is offline   Reply With Quote
Old 05-27-2012, 09:10 AM   #4
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Location: San Francisco, CA

Join Date: Feb 2011
Posts: 286

Those unmapped_left.fq.z files are not temp files. They do stay around after the run is complete and depending on how many reads you had in the first place and what percent successfully map, the files can be quite large. I believe tophat 1.x uses the .fq.gz format for these file while tophat 2 puts them in a .bam file. The bam files are more compressed than the .fq.gz. For my runs, I'm often finding the unmapped.bam is about 1/3 the size of accepted_hits.bam and ~2 GB (starting with ~50M PE 104bp reads). Gunzipped fastqs containing similar numbers of sequences might add up to 5 GB. If your doing RNAseq with the v3 kit, and starting with 100-150M PE 104bp reads, you might find the unmapped.bam getting up 5-8 GB, meaning fq.z files add up around 10 GBs. And you can safely get rid of these files if you're lacking for space. They will not effect the accepted_hits.bam file.

Now if you're finding the unmapped files are substantially larger than this, you might have a problem with the alignments in general. So, you might want to try some quality trimming or adjust bowtie settings to be more error tolerant.
Wallysb01 is offline   Reply With Quote

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