GOTHiC odd output
Entering edit mode
manduchi ▴ 10
Last seen 8 days ago
United States


I'm trying to test GOTHiC (version 1.6.0) on a dataset obtained from HiCUP, whose head is copied below. I'm using R version 3.2.2 with the following commands:

res=GOTHiChicup("hicup_2oligos.txt",sampleName="2oligos",res=100,"hg19_DpnII.txt",cistrans='all',parallel=TRUE, cores=8)

I noticed two problems:

1. The main one is with the resulting gothic_2oligos_100.txt file, whose head is also copied below.
The values under the columns chr1, locus1, chr2 and locus2 do not seem to make sense.

2. This is minor, but I thought the name of the .pdf file would be "2oligos.pdf", instead it's named Rplots.pdf.

Can anybody advice?

>head -4 hicup_2oligos.txt
K00283:24:H7VTLBBXX:1:1201:7273:17614   chr1    149895577 149895677
K00283:24:H7VTLBBXX:1:1201:7273:17614   chr12   57751831 57751918
K00283:24:H7VTLBBXX:1:1219:6360:46557   chr17   17380796 17380862
K00283:24:H7VTLBBXX:1:1219:6360:46557   chr17   17372834 17372934


>head -2 gothic_2oligos_100.txt

chr1 locus1 chr2 locus2 relCoverage1 relCoverage2 probability expected readCount pvalue qvalue logObservedOverExpected
0 0 13663252 13663300 1.92397622961321e-06 2.67093170699245e-05 1.02776350510097e-10 0.000454059133314474 1 0.000453956064089957 1 11.1048321838303
0 0 31033402 31033500 1.92397622961321e-06 2.26350144660377e-07 8.70986021272006e-13 3.84795875690232e-06 1 3.8479513535202e-06 1 17.9874752331921

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