Caleb Lareau comments

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                                            Caleb Lareau

Missing DIG_CTRL_per_barcode_metrics.csv.gz File

hey! thanks for the kind wishes. hope all is well with you!! I similarly can't find these files-- either I renamed them or they got eaten somewhere in the process....

rapidfuzz not present in bap Python package dependencies

thanks! is the fix as simple as adding this to the line that you noted?

bam file for bap2 input

Nope! there will be duplicate mark / removed during the execution of the basic pipeline

problem with python script

Hi, The tool was originally written with only python 2 support— that to me seems like the first thing to change (looks like you’re using python 3) On Mar 18,...

IOError: [Errno 2] No such file or directory: .log

Based on the last line I/O error, I think the error has to do with how you've specified the output path (I didn't write this to be terribly intelligent). Based...

Error determining peaks for anchor inference

Could you execute the command retaining intermediate files and then the `ls -lRh` of the directory?

"*_temporary_hichipperPeaks.bed_pad.bed.tmp" has size 0 issue

Try these two things 1) hopefully this works-- can you make sure that `bedtools` is in your environment? 2) Another potential issue is that your samples may not be calling...

Issue with MACS Output

Can you send your execution command + the ls -lR of the execution directory? > On Aug 13, 2019, at 4:35 PM, jlpulice wrote: > > Hi! > > I...

Issue with MACS Output

What are the contents of all.yaml? > On Aug 13, 2019, at 7:36 PM, jlpulice wrote: > > I'm running this with > hichipper --out hichipper_081319_test all.yaml > > For...

Issue with MACS Output

is `hg19_MboI_resfrag.bed` in your directory from execution? The process is failing when trying to compute the new hichipper-adjusted peaks.