Question: How do I find unmapped reads in my sam file?
0
gravatar for blur
2.6 years ago by
blur100
European Union
blur100 wrote:

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 • 1.9k views
ADD COMMENTlink modified 2.6 years ago by vivekbhr510 • written 2.6 years ago by blur100

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.

ADD REPLYlink written 2.6 years ago by rajasekargutha20
1
gravatar for vivekbhr
2.6 years ago by
vivekbhr510
Germany
vivekbhr510 wrote:

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

ADD COMMENTlink written 2.6 years ago by vivekbhr510

so, first turn it into bam, right?

ADD REPLYlink written 2.6 years ago by blur100

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by glihm590

thanks, that was super helpful! :)

ADD REPLYlink written 2.6 years ago by blur100
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