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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Bamcoverage and ATAC-seq #2302

Closed apastore closed 4 years ago

apastore commented 6 years ago

Hi @lpantano, I have seen that you are adding support for deeptools bamcoverage, thanks a lot for this, really nice. I was just wondering if these two parameter --extendReads 150 --centerReads could be not set as default, since I guess They maybe problematic with the ATAc-seq pipeline ?

Thanks a lot !

lpantano commented 6 years ago

Hi,

You are right and we are checking with some data the effect. Hopefully we can find the best values in a week or so.

Thanks!

lpantano commented 6 years ago

Hi,

sorry for the delay. @mistrm82 looked into some of our data and it looks fine with those parameters. If you have better ones and you can test it, i am happy to have separate values for each pipeline.

cheers

crazyhottommy commented 5 years ago

googled for something else and found this. want to chime in. for ATACseq, people may only want to pile up the Tn5 cut sites, if it is paired-end reads. only the 5' sites of each read are used, so --extendReads 150 may not be ideal.

ATACseq also gets read signal from mon- and di-nucleosomes in addition to the open chromatin regions. from the help page of bamCoverage

--minFragmentLength INT
                        The minimum fragment length needed for read/pair
                        inclusion. This option is primarily useful in ATACseq
                        experiments, for filtering mono- or di-nucleosome
                        fragments. (default: 0)

Although I am bit confused, is not --maxFragmentLength 147 should be used instead of --min?