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nh13 / DWGSIM

Whole Genome Simulator for Next-Generation Sequencing
GNU General Public License v2.0
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strand information in read ids? #20

Closed RichardCorbett closed 8 years ago

RichardCorbett commented 8 years ago

Hi. I know dwgsim isn't writting to simulate strand-specific RNAseq data. However, I thought I'd use it for a similar application where I only want reads from one strand.

Is it correct that we should have equal numbers of reads (within tolerance) from each of the strands?

I thought that I could figure out the strand of the simulated fragment by looking at the read ids where this id: @fastq-id_618_571_1_0_0_0_0:0:0_0:0:0_7/1 would be on the positive strand because the digit after "571" is a 1. However, I've since started to doubt this understanding because in my 10 million read fragments about 7 million have a 1 in that location.

Is there a way to get the strand of the simulated fragment from the read name?

nh13 commented 8 years ago

See if this helps: https://github.com/nh13/DWGSIM/wiki/Simulating-Reads-with-DWGSIM

RichardCorbett commented 8 years ago

Bingo. Missed that section when I read through earlier. thanks, RIchard

On 04/07/2016 11:25 AM, Nils Homer wrote:

See if this helps: https://github.com/nh13/DWGSIM/wiki/Simulating-Reads-with-DWGSIM

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nh13 commented 8 years ago

No problem, I am glad you are using it.