problem for merging 2 pairs of reads by "SeqPrep" tool
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.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
written by Sergio A.S. •
-
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
written by Eliveri •
-
HISAT2 error: Use of uninitialized value $l
written by sanchezgil.juanjose •
-
Error during pre-processing of RNA-seq reads for variant calling using Opossum/0.2
written by UDAY.AGRI123 •
-
problem for Collapsing Probes For Same Gene in microarray gene expression data
written by modarzi
-
how to match Ref. and Test data set genes for module preservation based on WGCNA?
written by modarzi
-
HISAT output SAM file incorrect (only contains 3 columns of data)
written by emcc •
-
Hisat2 versus Bowtie2
written by nalpas.nicolas •
-
Tophat 2 alignment error
written by cjvegame •
-
Fastq Quality Check
written by toshnam
