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.