Curiously, it's not listed as a tool on the docs: http://deeptools.readthedocs.io/en/latest/content/list_of_tools.html
fold enrichment calculation for exome sequencing
2 answers
plotEnrichment from deepTools can give you a nice plot of the fraction of reads in your target regions. Just give it a BED or GTF file and your BAM file.
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Devon Ryan
Oops, guess I never wrote the page for that!
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Devon Ryan
plotEnrichment -h will give the usage. Some example output is here, though note that the raw data can also be output. We mostly wanted this for FRiP scores and read distributions in RNAseq, but I'm sure there are other uses.
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Devon Ryan
Looks like we forgot the page for estimateScaleFactors too, though that's less interesting. I suppose I have my "to do" list for tomorrow.
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Devon Ryan
Read the docs should be updated shortly, thanks for finding my oversight!
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Devon Ryan
Thanks for the tool!
I am trying to run this but I am getting the below error. Anyone knows how to fix this?
Traceback (most recent call last): File "/home/anaconda3/envs/coverage/bin/plotEnrichment", line 12, in <module> main(args) File "/home/anaconda3/envs/coverage/lib/python3.7/site-packages/deeptools/plotEnrichment.py", line 522, in main verbose=args.verbose) File "/home/anaconda3/envs/coverage/lib/python3.7/site-packages/deeptools/getFragmentAndReadSize.py", line 111, in get_read_and_fragment_length fl = np.concatenate(imap_res) File "<__array_function__ internals>", line 6, in concatenate ValueError: need at least one array to concatenate
The --outRawCounts will have the counts written to a file of your choice.
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You are not really enriching for anything with exome sequencing.
Are you trying to determine coverage or maybe copy number alterations?
You are enriching for the exome... It's target enrichment. Perhaps he want to calculate average coverage in target region vs non-targeted sequences.
I should've been more clear. Yes, you are doing target enrichment, but "fold enrichment" implies comparing different samples or conditions. You can and should compare on- and off-target coverage, but it is not usually measured as a fold difference.