Eduardo Eyras

Please have a look at tximport: https://github.com/thelovelab/tximport to summarise the transcript quantification per gene to perform differential gene expression Best Eduardo On Fri, 5 Apr 2024 at 22:49, iamhealthy ***@***.***>...

Hi Arnav, could you please send me the GTF here: ***@***.*** ? In principle the format looks fine. But it was generated from a GFF, which has a single ID...

Thanks for sending the GTF file. The issue is what I suspected. The GTF does not contain multiple transcripts per gene. Using only the "exon" lines (used by SUPPA), I...

Hi Arnav, this means that the GTF annotation that you're using does not contain any alternative transcripts in the annotated genes, or that the variation of those transcripts cannot be...

Hi Chandaayan, your abundance file seems to have many zeroes. Do you get non-zero abundances for your transcripts? That could trigger some of the errors. E.

Hi Olivier, I managed to reproduce your problem. I looked at the .ioe and expression files, and saw that your expression file had a total 56980 different transcript IDs and...

Could you check if there are any events that have all the transcript IDs involved in the event in the expression file? My suspicion is that there isn’t, and that’s...

Hi, the ioe file defines the event by indicating the transcript that includes the alternative exon and the transcripts that include or exclude the exon, e.g.: 1 ENSMUSG00000026312 ENSMUSG00000026312;SE:1:110036685-110039327:110039381-110065592:+ ENSMUST00000134301...

Hi, I made a quick perl script to parse the expression and ioe file and check whether any of the transcript IDs in each event are missing, and all of...

Hi Yes, the ioe is fine I am wondering whether adding the ids with zeroes in the expression file might help E On Wed, 29 Mar 2023 at 21:46, Olivier...