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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
MIT License
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[Question] bam Coverage bw files clarification #948

Closed sunta3iouxos closed 9 months ago

sunta3iouxos commented 9 months ago

Hi Katarzyna, regarding the DNA-mapping and ChIP-seq pipelines there are few bw files created and I would like to know which ones are to be used for visualisation or other purposes (plots etc), so that comparisons can be done among samples. the files I see for my analysis that also include a spike in are:

A006850324_209957_S1_L000.filtered.seq_depth_norm.bw
A006850324_209957_S1_L000.host_scaled.BYhost.bw
A006850324_209957_S1_L000.host_scaled.BYspikein.bw
A006850324_209957_S1_L000.seq_depth_norm.bw

which ones are to be used if there is no spike-in organism and which with.

Is it also possible to add this information to the snakepipes info

katsikora commented 9 months ago

Hi,

if you wish to use spikein for normalization, then "A006850324_209957_S1_L000.host_scaled.BYspikein.bw" would be the way to go. Otherwise, "A006850324_209957_S1_L000.filtered.seq_depth_norm.bw", assuming there was filtering applied on the bam file level.

Sure, we can make the docs a bit more explicit .

Best,

Katarzyna

sunta3iouxos commented 9 months ago

Many many thanks.