Differential isoform usage

Dear SUPPA developers,

first of all: thanks a lot for providing your nice tool set!

I have one feature suggestion though: Since you have now included a script for the differential analysis of splicing events, and since SUPPA also reports PSIs per isoform, it would be nice to provide an analogous tool for differential transcript/isoform usage analysis, i.e. a tool that identifies robust isoform switches by making use of replicates and expression levels/abundances similar to diffSplice.

Any chance of getting that anytime soon? 😃

Thanks and best, Alex

[EduEyras]

Hi Michel,

Great to hear that you made it work. Thanks for letting me know.

cheers

Eduardo

On Mon, 29 Jul 2019 at 18:34, Michel van Elswijk [e-mail] wrote:

Hi Eduardo Eyras,

Last week I dug in the code and came to the discovery that my .tpm and .psi files had some issues. Fixed the file issues then the code worked just fine 👍 Thnx for the help!

cheers

Michel

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[EduEyras]

Hi Michel,

we have been using SUPPA2 with hg38 without any issues.

Have you checked whether there might be an issue with the haplotypes or duplicated annotations? hg38 contains haplotypes with the same gene ids and transcript ids. We usually do not include them in the analysis because of this ambiguity.

cheers

E.

On Tue, 23 Jul 2019 at 01:10, Michel van Elswijk [e-mail] wrote:

Hi Eduardo Eyras,

Thanks for your quick reply! I tried running SUPPA2 diffSplice in the same directory as the input files but without success:

test@testimagetest:~$ sudo python3 SUPPA-2.3/suppa.py diffSplice -m empirical -i ensembl_hg38.events.ioe -e R30DM_tpm_formatted.txt CEMWT_tpm_formatted.txt -p R30DM_events.psi CEMWT_events.psi -o CEMWT_R30DM_diffSplice

Calculating differential analysis between conditions: R30DM_events and CEMWT_events

ERROR:main:Unknown error: (<class ‘IndexError’>, IndexError(‘list index out of range’,), <traceback object at 0x7f91ba73dfc8>)

I tried the tutorial with hg19 successfully, but now with hg38 and some of my own samples, it suddenly starts giving me this “IndexError”.

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