Comparison of multiple groups in rMATS

[CCCBBG]

Excuse me, May I ask a question. I have the issue to compare AS events within several group. For example, I have groups A,B,C,D, and E. I want to find each group-specific AS events. Then group1 can be filled with A.bam. And group2 is B.bam, C.bam, D.bam,E.bam.Of course, these bam names are separated by "," in txt. Counld this design work?

[EricKutschera]

You can process all of your files with rMATS and then run any group comparisons that you're interested in. See this post: https://github.com/Xinglab/rmats-turbo/issues/398

[CCCBBG]

Thank you for your response. I was wondering if this application is correct. I am getting a lot of NA values. Almost all of the ASs have NA values in different groups. Is this reasonable? I am running with all the groups together.

python rmats.py --b1 "${TXT_dir}/all_samples_b1.txt" \ --gtf /home01/user/GRCh38/genes/genes.gtf \ -t paired \ --readLength 150 \ --nthread 45 \ --statoff \ --od "${output_dir}" \ --tmp "${output_dir}" \ --novelSS \ --libType fr-secondstrand

Some AS are not applicable in many groups, while in some, they are not applicable in a smaller number. How should we appropriately address this NA scenario? Looking forward to your reply.

[CCCBBG]

especially IncLevel1 column

[EricKutschera]

NA values in IncLevel1 happen if there are no reads to support that event for that sample. For cases where some of the samples don't have reads you could filter out those events or just use the groups that do have supporting reads