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owenjm / damidseq_pipeline

An automated pipeline for processing DamID sequencing datasets
http://owenjm.github.io/damidseq_pipeline
GNU General Public License v2.0
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replicate #13

Open rLannes opened 1 year ago

rLannes commented 1 year ago

Hi,

I have 2 replicate for my condition and 2 replicate for my control. how can I use damidseq_pipeline with my replicate?

marshall-lab commented 1 year ago

Hi,

Just run the pipeline once per replicate, so that you generate one output bedgraph per replicate.

Unfortunately there isn't an automated way for doing this at present (it's on the todo list). However, it's very easy to use a shell script to do this (which is one reason why it's never been added):

e.g. (in fish shell):

for i in 1 2 3; \
damidseq_pipeline sample_n$i.bam dam_n$i.bam; \
end; \

Typically, we tend to align all samples / reps at the same time (with the --just_align flag), then process the resulting bams as above.

Hope that helps, Owen