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jpromeror / EventPointer

R package for the identification and statistical analysis of alternative splicing events using junction arrays or RNASeq data
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errors in PrepareBam_EP #15

Open haiyueliu opened 2 years ago

haiyueliu commented 2 years ago

Dear EP developers,

I have triplet samples from multiple conditions. I could ran the PrepareBam_EP for samples from each condition separately. However, I always got errors if I run this for all bam files together. Here are the codes that I used:

bams <- dir(eventpointer.dir, pattern = "*.sorted.bam$") SG_RNASeq <- PrepareBam_EP(Samples = bams, SamplePath = eventpointer.dir, Ref_Transc = "GTF", fileTransc = gtf, cores = n.cores)

And the error message is:

Error in names(answer) <- dots[[1L]] : 'names' attribute [15] must be the same length as the vector [5] In addition: Warning message: In mccollect(jobs) : 10 parallel jobs did not deliver results

Do you know how to fix this error and how to combine different SG_RNASeq objects? Thank you.

Best, Haiyue

jpromeror commented 2 years ago

Hello @haiyueliu

Let me include @JFerrer-B to help you solve the problem.

Best!

Juan Pablo

JFerrer-B commented 1 year ago

Dear Haiyue,

I am very sorry for taking so long to reply. The error you mention is not very clear. It is strange that by separating the data the code worked for you but by putting the data together it did not. Could you please tell me the code you used to get the BAM files?

Juan