How do I find unmapped reads in my sam file?
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8.1 years ago
blur ▴ 280

Hi,

I want to see why my unmapped reads did not map to the reference - I wanted to pull out a few of the unmapped reads to blast them against the reference. Any idea how I do so? Thanks

SAM • 8.9k views
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hi, i am working on differential gene expression analysis on zebrafish datasets, i am working with GPL 14664 agilent platform but ther is annotation package available. i used limma package and i got results. but how to convert into gene symbols.

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8.1 years ago
vivekbhr ▴ 700

Use samtools. Just do samtools view -f 4 <bamfile> ..

You can extract all kinds of reads by specifying the flag No. after samtools -f . Get the relevant flags here

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so, first turn it into bam, right?

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It does not matter if the file is SAM or BAM formatted. Samtools view command is able to read both files. ;)

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thanks, that was super helpful! :)

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