Trouble while working with .csi indexes

[lorenzopanca5]

Hi everyone,

I am working on large genomes (durum wheat) which have chromosomes larger than the upper limit of 512 Mbp for the construction of .tbi index with tabix. I was wondering if there is an implementation in IsoTools that makes possible to work with non-Human genomes that require .csi indexes or a quick workaround of any sort.

Thank you for your time,

Lorenzo

[YalanBi]

Dear Lorenzo,

Thank you for contacting us.
I understand the problem with using Tabix to generate an index file. Could you please clarify which functionality in IsoTools2 you suggest using a .csi index as an alternative to a .tbi index for? If it is for importing the reference annotation, could you tell me whether you are using a gtf or gff/gff3 file?
Many thanks.

Regards,
Yalan

[lorenzopanca5]

Dear Yalan,

I had issues in the preparation of the transcriptome for alternative splicing events analysis. For now I only want to assign bam alignments to known transcripts, but i could not take advantage of my gff3 annotation file since .tbi index is not available.
Many thanks for your fast answer.

Lorenzo

[YalanBi]

Dear @lorenzopanca5,

Thank you for the information.
I think you could try the gtf option to import your annotaion. If you could convert your gff3 file to a gtf file, please have a try to import it into IsoTools2.
I hope this helps. Please feel free to let us know if you encounter any problems.

Regards,
Yalan