Flagstat On Bam Files

Question: Flagstat On Bam Files

7.7 years ago by

Slim Sassi • 60 wrote:

Hello, I tried to use NGS: SAM Tools ->flagstat on a BAM files for basic stats, but I got results like you see below. It doesn't seem to be working. Any suggestions? 26584869 in total 0 QC failure 0 duplicates 26584869 mapped (100.00%) 0 paired in sequencing 0 read1 0 read2 0 properly paired (-nan%) 0 with itself and mate mapped 0 singletons (-nan%) 0 with mate mapped to a different chr 0 with mate mapped to a different chr (mapQ>=5) Thanks Slim The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

• 2.2k views

ADD COMMENT • link •

modified 7.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.7 years ago by Slim Sassi • 60

7.7 years ago by

Sean Davis • 220

Sean Davis • 220 wrote:

Hi, Slim. My guess is that you used an aligner that outputs only aligned reads (tophat, for example) and that the input was single-ended. If that is the case, then what you see below is exactly as expected. If not, then you might need to be more specific about how you generated the BAM file. Sean

ADD COMMENT • link written 7.7 years ago by Sean Davis • 220

Sean, You are correct, I did use tophat. Can you or anyone suggest a program for BAM/SAM stats where the alignment was done with tophat Thanks Slim

ADD REPLY • link written 7.7 years ago by Slim Sassi • 60

for BAM/SAM stats where the alignment was done with tophat Slim, What stats do you want to capture? The output you gave for flagstats is correct for single-end tophat alignments. All reads are aligned, none are paired, none are marked as duplicates. Sean stats, but it is in

ADD REPLY • link written 7.7 years ago by Sean Davis • 220

Sean, I only wanted to start collecting stats with flagstats but knew that I needed something else to get everthing needed. I would like to know: % that didn't pass QC % mapped % reads in exons/introns/intergenic regions and then, knowing that this is more complicated, I wanted to measure bias within transcripts (for example 3' versus 5'). Of course I am assuming that there is a consistent bias. Thanks Slim

ADD REPLY • link written 7.7 years ago by Slim Sassi • 60

That information is not in the FASTQ files, so it will not be in the BAM files, generally. That information assumes that the aligner writes the the unaligned reads to the BAM file. Tophat does not do that. That is not something that flatstats provides. However, there are a number of other tools that could be coerced to give you this type of information (including Galaxy, probably). For this task, you may have to write some code unless someone else on the list is aware of a package that does this for RNA-seq data.

ADD REPLY • link written 7.7 years ago by Sean Davis • 220

Hello everyone I observed an issue when flagstat is incorporated in a workflow in which the BAM file it works on is also used by another program (generate pileup for instance) and is NOT the input dataset (generated by sam to bam within the workflow). I tested it with the local job runner and with TORQUE (with the pbs scheduler and Maui). - With the local job runner, it works just fine - With TORQUE I get the following error message: pbs_submit failed, PBS error 15033: No free connections Surprisingly, other non-linear workflows work fine. I only observed this error with flagstat. Moreover, when flagstat is in a linear workflow, it works fine too. Ad if it is non-linear but the input dataset is the bam file flagstat works on, it works fine too. Please find attached one of the test workflow where I found the error. The input dataset is a sam file. Any clue? Cheers, LA

ADD REPLY • link written 7.7 years ago by Louise-AmélieSchmitt • 160

Hi, This can most likely be fixed by increasing the value of NCONNECTS in the TORQUE source, in src/include/libpbs.h, and recompiling on your TORQUE server. I haven't seen a problem after increasing the value to 20. --nate

ADD REPLY • link written 7.7 years ago by Nate Coraor ♦ 3.2k

Le 06/04/2011 13:57, Nate Coraor a écrit : Hi, Sorry this is old but I tried recompiling torque after setting the NCONNECTS to 20 and the issue's still there. But there's more: It doesn't affect only flagstat but other non-linear workflows. One of the two jobs that are submitted when their "father" stopped running triggers the same error: PBS error 15033: No free connections And the best part is that it works fine sometimes. But when it crashes, it's always the same job that crashes. Does anyone have a clue? Cheers, L-A

ADD REPLY • link written 7.5 years ago by Louise-AmélieSchmitt • 160

Did you recompile both the client and the server? I am not sure which needs it, possibly both.

ADD REPLY • link written 7.5 years ago by Nate Coraor ♦ 3.2k

Similar posts • Search »