Read coverage for specific coordinates

Question

[Onkar]

Hi all,

I've N samples of Stomach Cancer having good read depth and I have run rMATS and DEXSeq on them. I have got the results successfully.

I have a test set (30 samples) for which read depth is not good, it's around 1 million read depth. I want to know how to calculate the read coverage or PSI values at a particular coordinate/location (i.e. for the coordinate which is found to be significant or the coordinate where there exist a difference between cancer vs non-cancer).

How do I do that?

The reason is I don't want to re-run rMATS on all 30 samples, because I know where difference could exist, and I just want to calculate PSI value at that event.

Please do let me know how to calculate PSI or read coverage at a particular coordinate. I have fastq files for 30 samples. Particular location I mean chr:start-end or rMATS based splicing event

Thanks

[Pierre Lindenbaum]

samtols depth -a -r "chr1:234-234" in.bam

[Onkar]

Hi, samtools depth: can't parse region "chr9:133320316-133376661" It gives me this error. :(

samtols depth -a -r "1:234-234" in.bam works... without chr

But @Pierre, I need to know read coverage and not read depth