How do I find unmapped reads in my sam file?

Question

[blur]

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

[rajasekargutha]

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.

Answer 1

[vivekbhr]

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

[blur]

so, first turn it into bam, right?

[glihm]

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

[blur]

thanks, that was super helpful! :)