Question: how to signify experiments/replica files in kissplice
0
gravatar for celine
7 months ago by
celine0
celine0 wrote:

I'm trying to follow the pipeline outlined at http://kissplice.prabi.fr/tools/kiss2rt/

I'm not quite certain how to signify different experiments / different replicas when using kissplice. For example, in trinity, this can be defined through a separate textfile, or in the command itself. Is there a similar syntax for kissplice?

Thank you!

kissplice snp • 292 views
ADD COMMENTlink modified 7 months ago by marchetcamille10 • written 7 months ago by celine0
1
gravatar for marchetcamille
7 months ago by
marchetcamille10 wrote:

Dear Celine, It is the order of the files that is taken into account. You can certainly give any name you want to your read files.

ADD COMMENTlink written 7 months ago by marchetcamille10
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gravatar for vincent.lacroix
7 months ago by
vincent.lacroix40 wrote:

Dear Celine, If you have 2 conditions and 2 replicates, which correspond to 4 fastq files, say c1r1.fq, c1r2.fq, c2r1.fq, c2r2.fq, then you can run kissplice with the following command

kissplice -r c1r1.fq -r c1r2.fq -r c2r1.fq -r c2r2.fq
ADD COMMENTlink written 7 months ago by vincent.lacroix40
0
gravatar for celine
7 months ago by
celine0
celine0 wrote:

Hi Vincent,
Just to be sure I understand completely... is kissplice parsing the order of the inputs or the names of the files? If the later, is it looking specifically for the c's and r's, or does it look for matches? (e.g. I could put exp1rep1, exp1rep2...) Thanks for your help!

ADD COMMENTlink written 7 months ago by celine0
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