fold enrichment calculation for exome sequencing

Question

[bitpir]

Hi, I was wondering if there's a software available for calculating fold enrichment for exome sequencing? I see that USEQ's intersect region can calculate fold enrichment, but mostly for Chip-seq. I was wondering if I can use that for exome data? Thanks!

[igor]

You are not really enriching for anything with exome sequencing.

Are you trying to determine coverage or maybe copy number alterations?

[WouterDeCoster]

You are enriching for the exome... It's target enrichment. Perhaps he want to calculate average coverage in target region vs non-targeted sequences.

[igor]

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.

Answer 1

[Devon Ryan]

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.

[igor]

Curiously, it's not listed as a tool on the docs: http://deeptools.readthedocs.io/en/latest/content/list_of_tools.html

[Devon Ryan]

Oops, guess I never wrote the page for that!

[GenoMax]

Is there inline help for this? I want to try this out.

[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.

[igor]

This is the greatest easter egg ever.

[Devon Ryan]

Read the docs should be updated shortly, thanks for finding my oversight!

[igor]

Thanks for the great tool.

[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.

[CL]

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

Answer 2

[bitpir]

Hello Devon, Thank you so much! This is what I am looking for. I was wondering if there's anyway to display the enrichment values on the graph as well? Or simply having the values itself as a different file would suffice. Thanks again! Lora

[GenoMax]

Please use ADD COMMENT/ADD REPLY when providing additional information/replying to existing posts. SUBMIT ANSWER should only be used for new answers to original question. This comments belongs up against @Devon's answer.

[Devon Ryan]

The --outRawCounts will have the counts written to a file of your choice.

[bitpir]

Thank you so much for tip, it is a great tool indeed! :)