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sarahhainer / uliCUT-RUN

Example scripts for analyzing CUT&RUN datasets
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trimming and barcode #2

Open nservant opened 4 years ago

nservant commented 4 years ago

Hi, Could you help me understanding why you trimmed to 25bp, and why you look for barcodes in your reads ? Is there somewhere a schema of the library prep / reads content to better understand those points ? Many thanks

sarahhainer commented 4 years ago

Hi,

This is entirely dependent on what adapters you add whether you need to split barcodes/trim off. We were using old school inline PE adapters where Illumina platforms couldn't split these automatically on BaseSpace. Now using other adapters this is unnecessary. But we typically trim down to 25bp because this is inline with Henikoff sequencing on 24bp runs.

We have our paper on CUT&RUN protocol here: https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpmb.85 Henikoff also has protocols available too: https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn; https://www.nature.com/articles/nprot.2018.015