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dieterich-lab / JACUSA2helper

Auxiliary R package for assessment of JACUSA2 results
https://dieterich-lab.github.io/JACUSA2helper/
GNU General Public License v3.0
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Compare multiple replicates of multiple conditions #11

Open meservey opened 3 years ago

meservey commented 3 years ago

I am interested in comparing RNA editing across multiple conditions with replicates of each condition. I have only found that JACUSA2 is able to compare at most 2 conditions with one condition having a single replicate. Is there a way to compare multiple conditions with multiple replicates?

piechottam commented 3 years ago

JACUSA2 supports 1 and 2 condition comparisons (call-1 and call-2). Each of these modes supports an arbitrary number of replicates (0 - n).

Comparison of more than 2 conditions is currently not supported out of the box.

d-fuh commented 1 year ago

Hello, we currently have a similar set up with 2 conditions and n replicates in each condition (with a total of 2n bam files with the same reference fasta). I am wondering what the command would look like for this situation using call-2? I couldn't locate it in the manual. Thank you in advance for your help!

piechottam commented 1 year ago

Dear User,

you need to join your bams per condition with ",": jacusa2.jar call-2 [OPTIONS] cond1_1.bam,cond1_n.bam cond2_1.bam,cond2_n.bam