Question: how to signify experiments/replica files in kissplice
0
gravatar for celine
11 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 • 396 views
ADD COMMENTlink modified 11 months ago by marchetcamille10 • written 11 months ago by celine0
1
gravatar for marchetcamille
11 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 11 months ago by marchetcamille10
0
gravatar for vincent.lacroix
11 months ago by
vincent.lacroix50 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 11 months ago by vincent.lacroix50

Hi Vincent , Is it advised to merge paired end read files of a sample to one fastq file and further feed it for kissplice analysis? Cos when 2 read files of a sample are treated as 2 samples it gives allele frequency separately. How to resolve this ? And it would be clear if further detailed information pertaining to the outputs are given in manual .

Thank you

ADD REPLYlink written 12 weeks ago by koushikponnanna0
0
gravatar for celine
11 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 11 months ago by celine0
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: 873 users visited in the last hour