Daniel Kim comments

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                                            Daniel Kim

Can this pipeline be used for analyzing paired-end 75bp reads?

Yes this can!

Comparing Treatments with Multiple Paired End Replicates

Hi llz-hiv, please repost this as a separate issue, as this is not related to the above thread. Also please consider subscribing to our pipelines google group, which may have...

UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 30

Hi, could you pass in the tail end (or full) BDS log file? (Should end in *.log). Looks like a unicode error when the ATAQC module is writing out the...

UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 30

Thanks for the log - that was helpful! It looks like there's some issue with setting up the filename, which I'm extrapolating to think that there may be some nonstandard...

UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 30

interesting - it could be related to a different output format from a different version of ucsc tools - can you provide the top of the *signal file in the...

slopBed chromsizes filter on raw MACS2 output

I've asked the person for the file - see https://github.com/kundajelab/atac_dnase_pipelines/issues/50 - I'll give it a try and let you know, though it seems pretty clear that MACS2 is outputting a...

Steps between pipeline and diffE

Hello, We prefer to use the tagAlign files, which are BED formatted files of the reads (ie, each line in the file is a different read). We then use bedtools...

Incompatibility with samtools version 1.3

Hi, Thanks for the heads up. We'll do both - document for now, and if any patches come our way we're happy to accept! :)

Unable to run after following installation instructions

Hi, Confirming the above error, I ran into this exact thing as well. I tried what Ian suggested and ran the test in a different directory and the test ran...