Question: Difference In Number Of Reads Using Samtools View And Igv
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gravatar for pm2013
6.4 years ago by
pm201350
pm201350 wrote:

Hi

I extracted reads from a specific region from tophat alignment (bam files) using samtools view. The number of reads I get is 20. When I checked the region using IGV, the only subset of reads actually pass thorough the region. There are few reads that clearly end before the start of the region that I specified. I am very perplexed with this. Someone please enlighten me. Thanks

samtools rna-seq igv • 2.7k views
ADD COMMENTlink modified 27 days ago by Biostar ♦♦ 20 • written 6.4 years ago by pm201350
0
gravatar for Istvan Albert
6.4 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

IGV ocassionally shows crazy things if it starts to run out of memory. Make sure that is not the case.

In general trust samtools first. You can verify from the coordinates whether the selection is correct.

ADD COMMENTlink written 6.4 years ago by Istvan Albert ♦♦ 81k
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gravatar for Steve Lianoglou
6.4 years ago by
Steve Lianoglou5.0k
US
Steve Lianoglou5.0k wrote:

Perhaps IGV is only showing reads flagged as primary alignments (the 0x100 bit in the FLAG) and samtools is showing all?

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Steve Lianoglou5.0k
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gravatar for Chris Miller
6.4 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

Are your reads trimmed or soft-clipped? If so, it's possible that one program is respecting that and the other is not.

ADD COMMENTlink written 6.4 years ago by Chris Miller21k
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gravatar for Zhen Sun
6.4 years ago by
Zhen Sun50
Durham, NC, USA
Zhen Sun50 wrote:

IGV will hide soft-clipped base pairs by default. You can turn on "show soft clipped reads" in IGV's preferences panel and see if the result matches with samtools.

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Zhen Sun50
0
gravatar for Gabriel R.
6.4 years ago by
Gabriel R.2.6k
Center for Geogenetik Københavns Universitet
Gabriel R.2.6k wrote:

I think that igv only shows the reads that passed QC, try using samtools view -F"0x200" to check if you get the same reads.

ADD COMMENTlink written 6.4 years ago by Gabriel R.2.6k
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