Question: How can I extract sequence from a SAM file, with coordinates
0
gravatar for SaltedPork
2.9 years ago by
SaltedPork100
SaltedPork100 wrote:

Lets say I have chr1:65355-65398, how do i get the reads that cover this region out of the SAM? I've converted to BAM, sorted it, then indexed it, then i run it with:

samtools view align_sorted.bam chr1:65355-65398

But i return nothing, so either there''s no read in that region, or I've done something wrong along the way.

samtools view -bS align.sam > align.bam
samtools sort align.bam align_sorted.bam
samtools index align_sorted.bam align_sorted.bai

^^ Are the other commands I used.

sam samtools • 1.9k views
ADD COMMENTlink written 2.9 years ago by SaltedPork100
1

The command looks correct. The file probably does not contain the region. Just do a positive control:

samtools view in.bam | head -n 10

Then enter the chr and coords from the first entry and check if it is returned sucessfully.

ADD REPLYlink written 2.9 years ago by ATpoint24k
1

and check it's 'chr1' and not just '1'

ADD REPLYlink written 2.9 years ago by Pierre Lindenbaum123k
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