Hi,
Currently I'm trying to solve a simple problem for bioinformatician, but being a experimental biologist it's proving to be very tricky for me.
At the moment I've obtained mapped reads in SAM format. I want to determine the sequencing coverage in term of number of times sequenced per base. I know I can use pileup function in samtool however it does not give strand specific information.
Are there any way of counting the bases per strand?
Or perhaps handling the pileup dataset in Galaxy to obtain strand specific count?
Many help would be great thank you.
Currently I'm trying to solve a simple problem for bioinformatician, but being a experimental biologist it's proving to be very tricky for me.
At the moment I've obtained mapped reads in SAM format. I want to determine the sequencing coverage in term of number of times sequenced per base. I know I can use pileup function in samtool however it does not give strand specific information.
Are there any way of counting the bases per strand?
Or perhaps handling the pileup dataset in Galaxy to obtain strand specific count?
Many help would be great thank you.
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