how to signify experiments/replica files in kissplice

Question

[celine]

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!

Answer 1

[marchetcamille]

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.

Answer 2

[vincent.lacroix]

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

[koushikponnanna]

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

Answer 3

[celine]

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!