problem: i try to merge reads with seqprep but is not working
0
0
Entering edit mode
3 months ago
Nalid • 0

Hi everybody I want to merge reads (reverse and forward) so I use seqPrep with this command :

seqprep -f SRR_1.fastqsanger.gz  -r SRR_2.fastqsanger.gz  -1 forward.fastq -2 reverse.fastq -s gunzip merged_file.fastq

Pairs Processed:    0
Pairs Merged:   0
Pairs With Adapters:    0
Pairs Discarded:    0
CPU Time Used (Minutes):    0.000004
seqprep • 222 views
ADD COMMENT
0
Entering edit mode

What is your question? Also, can you please think of a more informative title for your question?

ADD REPLY
0
Entering edit mode

i dont know why my command not working!

ADD REPLY
0
Entering edit mode

What kind of data are you working with? Since Pairs Processed says zero it appears that your command is not working. Are the data files in the directory where you are running this in? RNAseq datasets do not necessarily merge (unless they have short inserts) so is this really what you want to do?

ADD REPLY
0
Entering edit mode

I'm working on RNAseq metatranscriptomics , I want to merge them ( how can i know if they have short or long insert?)

ADD REPLY
0
Entering edit mode

You can try the method suggested here to estimate size of inserts in your library: Target fragment size versus final insert size It is not necessary that your reads are going to merge since it will depend on the library insert size.

You can use bbmerge.sh from BBMap suite to try the merging as well.

ADD REPLY

Login before adding your answer.

Traffic: 1886 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