aryeelab
About Macs2 parameter
Hi， I have use this software well . However , I failed to pass parameter to MACS2 . For example ,I just want to change "p" value from 0.01 to 0.0001 as " --macs2-string "-q 0.0001" " or " --macs2-string -q 0.0001" But I got Error: Got unexpected extra argument (0.0001) Why? What can I do ? Thanks!
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 AM, werhoog [email protected] wrote:
I check it many times. But I cannot find any problems. Why?
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hichipper --out hichipperpol21 yaml/one.yaml --macs2-string -q 0.0001 --extsize 147 --nomodel --macs2-genome mm --peak-pad 1000 --merge-gap 1000 --keep-temp-files --make-ucsc
And what’s the specific error for this command?
On Mar 20, 2018, at 8:58 AM, werhoog [email protected] wrote:
hichipper --out hichipperpol21 yaml/one.yaml --macs2-string -q 0.0001 --extsize 147 --nomodel --macs2-genome mm --peak-pad 1000 --merge-gap 1000 --keep-temp-files --make-ucsc
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Yean, I think it is I only pass "-p" that caused this problem. So I pass --macs2-string -q 0.0001 --extsize 147 --nomodel . And it said "Error: no such option: --extsize" and quit I used python 2.7.14
I guess I have solved it by moderate cli.py from 0.01 to 0.0001 . And this program runs well. Thank you all the same. By the way, if I want to use Hic-Pro output results , does this program runs with only using *Allvalid.pairs (for at most time, only allValid.pairs counts).I have put only allvalidpairs to HiChipper,and it worked.But I got too many peak(more than one hundred thousand). So,should I put all pairs(include self-cycle pairs,DEPairs and so on ) to hichipper? Will this cause to use pairs ont only allValidpairs ?
Thank you!
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 reducing the number of peaks (https://www.biorxiv.org/content/early/2017/09/21/192302 https://www.biorxiv.org/content/early/2017/09/21/192302)
On Mar 22, 2018, at 3:52 AM, werhoog [email protected] wrote:
I guess I have solved it by moderate cli.py from 0.01 to 0.0001 . And this program runs well. Thank you all the same. By the way, if I want to use Hic-Pro output results , does this program runs with only using *Allvalid.pairs (for at most time, only allValid.pairs counts).I have put only allvalidpairs to HiChipper,and it worked.But I got too many peak(more than one hundred thousand). So,should I put all pairs(include self-cycle pairs,DEPairs and so on ) to hichipper? Will this cause to use pairs ont only allValidpairs ?
Thank you!
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I didn't do anything but change the scripy of cli.py under hichipper fold. Thant is to say ,I changed the default parameter of 0.01 to 0.0001.