Question: Make Paired File Task-Scripture
gravatar for GPR
7.0 years ago by
GPR320 wrote:

Hello, I am trying to prepare the input file for Scripture and have stumbled upon the fact that I need to have the TopHat alignment output split into right and left reads. Can somebody tell me how to do this? I obviously had a bam file,containing both right and left reads. Thanks, G.

ADD COMMENTlink modified 4.1 years ago by Biostar ♦♦ 20 • written 7.0 years ago by GPR320
gravatar for Istvan Albert
7.0 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

I think you could get that information from the SAM file. the spec says that column 8 PNEXT indicates the position of the mate/next segment.

So for each line if the position is larger than the current position then it is a left read otherwise a right read.

ADD COMMENTlink written 7.0 years ago by Istvan Albert ♦♦ 81k

Thanks a lot, I will look into this.

ADD REPLYlink written 7.0 years ago by GPR320
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