Metrics of percentage of reads mapped to intron and exon

[MengjunWu]

Hi,

I was wondering if it is possible to include metrics like percentage reads mapped to intron and exon regions from the star solo output -- as the mapping metrics in 10x web summary. We found these metrics are useful for quality control our single nuclei data. I used GeneFull mode but did not find such information in the Summary file.

Many thanks!

Best, Mengjun

[alexdobin]

Hi Mengjun

you can generate such output by comparing Gene and GeneFull statistics, since Gene counts only exonic reads, and GeneFull counts exonic+intronic. You can get both outputs in one run with --soloFeatures Gene GeneFull. Also, the best match to CellRanger results is achieved with GeneFull_Ex50pAS option.

[MengjunWu]

Thanks for the reply, Alex!

I did not use GeneFull_Ex50pAS for the last run, can I recount with GeneFull_Ex50pAS option using just output bam files from star solo -- I see some options allow users to use bam (from 10x) as input file, however not sure if this applies for recounting purpose. For recounting, should one keep all other parameters the same as using fastq as the input files ?

Thanks, Mengjun

[alexdobin]

Even if you use BAM files as input, STAR will remap the reads, so it will be no faster (probably slower) than using FASTQ input.

[MengjunWu]

Got it, thanks a lot!

On Tue, 17 Oct 2023 at 16:32, Alexander Dobin @.***> wrote:

Even if you use BAM files as input, STAR will remap the reads, so it will be no faster (probably slower) than using FASTQ input.

— Reply to this email directly, view it on GitHub https://github.com/alexdobin/STAR/issues/1970#issuecomment-1766544210, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEG6WNVX3LB3WBZY7OHHYOLX72JI3AVCNFSM6AAAAAA6DXGMQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONRWGU2DIMRRGA . You are receiving this because you authored the thread.Message ID: @.***>