Question: Use jellyfish with paired end sequencing data
0
gravatar for db
19 months ago by
db0
USA/Lincoln/UNL
db0 wrote:

I am wondering how exactly we should run jellyfish to count k-mers for paired end sequencing data. Is it enough to concatenate the forward and reverse read (using cat) or do we need to merge the reads (using something like PEAR)?

jellyfish • 1.2k views
ADD COMMENTlink modified 19 months ago by Brian Bushnell16k • written 19 months ago by db0
2
gravatar for Brian Bushnell
19 months ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

Concatenating the files works fine (I think you can just give it multiple files, but the syntax in the help message is a little confusing). Merging the reads is also a possibility, but you don't really need to do so in this case, and note that it would change the counts and yield even more files (merged, r1 unmerged, r2 unmerged).

ADD COMMENTlink modified 19 months ago • written 19 months ago by Brian Bushnell16k

Thank you Brian. Are you saying it is ok to concatenate based on your experience (not that I don't trust you)? It's just that I could not find any documentation on how to deal with paired end data.

ADD REPLYlink written 19 months ago by db0
1

For pure kmer counting, read pairing does not matter, and concatenated fastq files are still valid fastq files. I have never actually concatenated two files and then run Jellyfish on the result, but I have done that with various other programs.

ADD REPLYlink written 19 months ago by Brian Bushnell16k

Thanks you very much!

ADD REPLYlink written 19 months ago by db0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1275 users visited in the last hour