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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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setting for cutandrun #909

Closed sunta3iouxos closed 1 year ago

sunta3iouxos commented 1 year ago

Hi all, How am I setting specific commands for the cut and Run in the ChIP-seq pipeline? the cut and tag is specific for the tn5 transposase that adjusts the fragments for +5/-7 (if I recall correctly) but MNAse is a bit different? Thank you

katsikora commented 1 year ago

Hi sunta3iouxos,

you can run both DNA-mapping and ChIP-seq workflows with the --cutntag flag. This will adjust mapping and peak calling settings, accordingly. Also, if you've got spikein in your samples, you might want to map to a hybrid genome (that can be generated with createIndices) and the pass --useSpikeInForNorm in the ChIP-seq workflow.

We don't do any adjustments on the mapped fragment positions as is.

Best wishes,

Katarzyna

sunta3iouxos commented 1 year ago

Hi Katarzyna, so no necessary adjustments for the cut&run protocol. thank you!