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estepi / ASpli

Analysis of alternative splicing using RNAseq
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jCounts error #18

Open vinothkr11 opened 3 years ago

vinothkr11 commented 3 years ago

Hi Estefania, I am running into multiple errors with the jCounts function.

First I had a "NAs are not allowed in subscripted assignments" error - that I was able to overcome by removing NAs from the joint counts in the ASpli counts dataset.

Now, I am getting the following error

"Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'merge': no rows to aggregate"

Do you think I should get rid of the ChrUN as most of the warnings are related to it?

Thanks.

vinothkr11 commented 3 years ago

Also, my gene count and bin count values are all zero.

estepi commented 3 years ago

Hi, thanks for using ASpli!

In order to help you, can you tell me please:

-Chromosome names are the same in your alignment and your anntoation ? You can use:

seqlevels(genomeTxDb)

And for bam files:

samtools view -H your.bam

-Which genome is it?

Yes, I would avoid as much as possible "not confident" annotations, assemblies... (ChrUN)

Can you paste your doubt here, so more people can contribute to solve this issue?

https://support.bioconductor.org/

thanks a lot!