issue with single cell mode in 3.6.0-sc

[SuiYue-2308]

Hi IsoQuant team,

Thank you for developing IsoQuant!

I have tried IsoQuant in a single cell data. And I use the version 3.6.0-sc which is suggested in one of the issues. Then I found it reporting the error like "KeyError: 'unknown reference 1'. and also "unknown reference chrIS".

I have double checked that the gtf file and fasta file are matched. Do you have any idea that how can I fix this problem? Thank you so much!

[andrewprzh]

Dear @SuiYue-2308

There is a newer version in the branch sc_3.7, however, it's also an alfa version and may have some issues. Could you also check you BAM file header? Newer version will automatically check you reference genome, GTF and BAM in terms of chromosome name consistency.

Best Andrey

[SuiYue-2308]

Hi Andrey,

Thank you for your reply! Let me try the new version!

Best, Yue

[SuiYue-2308]

Hi Andery,

I have tried the sc_3.7. Just want to confirm whether this version need fastq file for single cell data (--mode tenX)?

Best, Yue

[andrewprzh]

Hi @SuiYue-2308

Similarly to usual IsoQuant, you can use FASTQ or BAM as an input.

Best Andrey