problem for merging 2 pairs of reads by "SeqPrep" tool
0
0
Entering edit mode
4.5 years ago
modarzi ▴ 170

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.

seqprep rna-seq • 989 views
ADD COMMENT

Login before adding your answer.

Traffic: 3119 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6