Question: problem for merging 2 pairs of reads by "SeqPrep" tool
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gravatar for modarzi
11 months ago by
modarzi130
modarzi130 wrote:

For Data processing In GSM1827405 author wrote that "Overlapping reads were merged using SeqPrep and split in half with a Awk routine. Paired-ends with one read shorter than 30 bp were discarded." I run below code in my Linux:

seqprep -f SRR2017741_1.fastq.gz -r SRR2017741_2.fastq.gz -1 SRR2017741_1_seqprep.fastq.gz -2 SRR2017741_2_seqprep.fastq.gz

and I get below result:

Pairs Processed: 37404976 
Pairs Merged: 0 
Pairs With Adapters: 75653
Pairs Discarded: 28621

I don't know why Pairs Merged is 0? I appreciate if anybody shares his/her comment with me for finding my problem and completing my "seqprep" code for this sample.

rna-seq seqprep • 229 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by modarzi130
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