Caleb Lareau
Caleb Lareau
everything looks fine from my end ``` hichipper --out output1 yaml/one.yaml Mon May 14 23:30:04 EDT 2018: Starting hichipper pipeline v0.7.2 Mon May 14 23:30:04 EDT 2018: Parsing user parameters...
Out of curiosity, what did you wind up doing to fix this?
Yeah, I made these files as a straight plug-and-chug from HiC-Pro data. I think that I used the HiTC package rather than the python scripts provided in the documentation. I'm...
What’s the exact hichipper command that was run? Your error indicates that it’s associates with the “string”... you don’t actually need any quotes > On Mar 20, 2018, at 8:28...
And what’s the specific error for this command? > On Mar 20, 2018, at 8:58 AM, werhoog wrote: > > hichipper --out hichipperpol21 yaml/one.yaml --macs2-string -q 0.0001 --extsize 147 --nomodel...
That’s great… Could you share the command that you used that wound up working? I’m actively working to change the input now, but see our supplement about different ways of...
The # of mapped unique quality interactions is derived from this: ``` cat "${WK_DIR}/${HICPRO_OUT}/hic_results/data/${SAMPLE}/"*Pairs | wc -l | awk '{print $1}' ``` What version of HiC-Pro are you using?
@werhoog can you provide your `.stat` files?
Hi Rola, Yes, I've been meaning to expand-- this seems straightforward enough. Could you possibly provide a sample .bam file of say chromosome 22 (human) OR chromosome 19 (mouse) from...
Sure thing-- [email protected]