problem: i try to merge reads with seqprep but is not working

Question

[Emy Alade]

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

[seidel]

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

[Emy Alade]

i dont know why my command not working!

[GenoMax]

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?

[Emy Alade]

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

[GenoMax]

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.