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RitchieLabIGH / IRFinder

MIT License
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System limitation: 32GB RAM #14

Closed mguaita closed 2 years ago

mguaita commented 2 years ago

Hello,

Is it possible to run IRFinder on a local computer with just 16 GB of RAM?

Thank you very much

CloXD commented 2 years ago

Hello Maria, the limiting step for the RAM is the mapping with STAR. Using a different alignment software can be a solution to your problem, then you just have to give the BAM file as input of the "IRFinder BAM" command as described here. Cheers, Claudio

mguaita commented 2 years ago

Dear Claudio, Thank you, it worked just fine.

so actually, the RAM is just a requirement for the steps of building the reference (in my case I chose: "BuildRefProcess") and quantify IR from FASTQ, is that correct?.

Also, to continue with the Differential IR Analysis, I do not understand the Usage command line with DESeq2: IRFinder Diff -g:Group1 ./Group1/Sample/IRFinder-IR-nondir.txt -g:Group2 ./Group2/Sample/IRFinder-IR-nondir.txt [-g:Group3 ...] https://github.com/RitchieLabIGH/IRFinder/wiki/Differential-IR-Analysis-With-Replicates

how do I write the command line for Diff mode including more than one sample/replica on each group? or is the input just one IRFinder output per group? If so, ¿how do I generate one IRFinder output per group with the BAM mode?

CloXD commented 2 years ago

Dear Maria, yes, that's correct, all the steps that depends on STAR inherit it's RAM requirements. For what concerns the Diff command, it's supposed to work with at least 3 samples for each group ( otherwise you can use the Audic and Clavier test ) . The different samples for each group can be given as space separated list. In bash the asterisk * is expanded to match the existing paths. In the example, suppose to have three subdirectories for each group called Sample_1, Sample_2 and Sample_3, the command

IRFinder Diff -g:Group1 ./Group1/Sample*/IRFinder-IR-nondir.txt -g:Group2 ./Group2/Sample*/IRFinder-IR-nondir.txt

Is be interpreted as:

IRFinder Diff -g:Group1 ./Group1/Sample_1/IRFinder-IR-nondir.txt ./Group1/Sample_2/IRFinder-IR-nondir.txt ./Group1/Sample_3/IRFinder-IR-nondir.txt  -g:Group2 ./Group2/Sample_1/IRFinder-IR-nondir.txt ./Group2/Sample_2/IRFinder-IR-nondir.txt ./Group2/Sample_3/IRFinder-IR-nondir.txt

Cheers, Claudio

mguaita commented 2 years ago

Thank you very much Claudio!