Merged genes output

[SergioManzano10]

Description of the bug

When I run the rnasplice pipeline and I get the result about differential exon usage, I get a table of counts.

I have used the ENSEMBL files (fasta and gtf) to generate the sashimi plots. However, when I look at the counts table mentioned above, for some genes (like BRCA1) I get "merged" identifiers (e.g. ENSG00000267002+ENSG00000012048), so I don't know the exon counts that correspond to each gen.

I think it is due to overlapping positions.

How could I solve it?

Thank you.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[jma1991]

You are correct; the merged identifiers are generated when there are overlapping exons. You can find the exon-level counts in the featurecounts directory. Additionally, these counts are available in the DGEList object from the edgeR analysis and the DEXSeqDataSet object from the DEXSeq analysis.

[SergioManzano10]

Is the same if I set the - - aggregate parameter to false? El El lun, 20 may 2024 a las 21:29, James Ashmore ***@***.***> escribió:

…

You are correct; the merged identifiers are generated when there are overlapping exons. You can find the exon-level counts in the featurecounts directory. Additionally, these counts are available in the DGEList object from the edgeR analysis and the DEXSeqDataSet object from the DEXSeq analysis. — Reply to this email directly, view it on GitHub <#139 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BENHAIDLCOP5ALWIEEGGQHTZDJFHZAVCNFSM6AAAAABH7UB7RCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRRGA3DONJUGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[SergioManzano10]

I did with - - aggregate parameter set to false and worked.

I will close the issue.