Entering edit mode
3.2 years ago
ashafik
•
0
I'm trying to get the number of reads that start at a given position. I'm using bbmap pileup.sh. This is the script:
./pileup.sh in=sorted.bam basecov=coverage.txt startcov=t
How can I get coordinate information. For example, chrM 1033: 10 (so 10 reads start at that position).
Thank you
Thanks for the reply. This is the output I get:
Since you used
should produce counts on reads that start at that position. Is this not working?
It's not working for me. I just get the output that I showed. The pos column goes to 187588718 and counting. The other two columns don't change.
Are you sure
sorted.bam
has alignments? I testedpileup.sh
with a file I had and was able to get counts. Can you show output ofsamtools view sorted.bam | head -6
?What do you mean by alignments? Here is the output:
The alignments look fine. Looking at this you should get something in your coverage file around
3014930
in second column.If you do
grep 3014930 coverage.txt
what do you see?Yes I see counts now. Thank you for your time.