Analyze coverage on each chromosome

[sindrle]

Hi!
We have sequenced up some single cells, but now I have to check the amount of rRNA/tRNA/chrM and how much coverage we actually have on known genes (per chromosome or something similar).

How do you people usually do this? I have been playing around with Igvtools count etc. But I want hard data i.e. 60% chrM reads and X reads on chr1 etc.

We only have 20 mill. reads per sample and only 8 samples. What is considered ok coverage with regards to genes we want to analyze (non-rRNA/tRNA/chrM)?


Thanks!

[GenoMax]

Bedtools coverageBed should suffice. Search for threads on the forum that cover this with examples etc.

[sindrle]

Oh, I just didnt use the correct search terms, thanks!

I have also played around a bit with Seqmonk, but I didnt quite like it at first glance.. Maybe BEDtools is the way to go.

This one is good:

http://seqanswers.com/forums/showthread.php?t=41110&highlight=coverageBed