apply isoquant to single-cell long read data

[linalu1121]

HI,

Thank you for developing this tool.

I'm trying to use this tool on single cell long read data. I have individual bam file for each cell barcode, around 3000 bam files in total.
Then I use these 3000 bam files as input, but I got error " Too many open files in system", even I have set the ulimit to 1 million (1,000,000) for the maximum number of open files.

Do you have any suggestions to deal with this situation?

[andrewprzh]

Dear @linalu1121

Did you use ulimit -n to set the limit? Could you send me the log file?

The possible workaround that comes to mind is to merge these BAM files into a single one, keeping read barcode e.g. in BC tag and specifying read grouping policy via --read_group.

Best
Andrey

[linalu1121]

Thanks, Andrey.
Yes, I use ulimit -n to set the limit.
I have tried to use cell barcodes in bam files to group feature counts. It works! Thanks for suggestion.

Lina