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ChangLab / FAST-iCLIP

Fully Automated and Standardized (FAST) iCLIP analysis pipeline.
GNU General Public License v2.0
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Single-End reads? #29

Closed marencc closed 7 years ago

marencc commented 7 years ago

Dear Developer,

My congratulations for this excellent pipeline. I would like to know if your pipeline is enabled for single-end reads. In the lab I am working, they preferred single-end for budget purposes. It is not enabled, what changes would you suggest that I do, so that I can analyze my data? (Or else, Is there a problem if I just have single-end reads?)

Also, is it necessary to have, at least two replicates?

Many thanks for your help and support!

Maria

bdo311 commented 7 years ago

1) The pipeline is single-end by default so you should have no problem.

2) Generally it's nice to have at least 2 replicates in order to maximize robustness, but if you only have 1 you can split your fastq file into 2 equal pieces.