Closed Lucas446 closed 1 year ago
Hi, You may have an empty line in your file. Could you do a tail of your bed file? Thanks
Hi Lucille,
Thanks a lot for your reply, that was actually this issue :)
Best, Tanguy
Le ven. 4 nov. 2022 à 02:20, Lucille Delisle @.***> a écrit :
Hi, You may have an empty line in your file. Could you do a tail of your bed file? Thanks
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Hi,
I am using HiCexplorer hicAggregateContacts function to get the contacts between a set of genomic positions (.bed file).
head of my bed file:
first line of the validPair.bam:
HiCexplorer command for hicAggregateContacts:
hicAggregateContacts -m ${FILE} --outFileName norm_smallest_esc_CyO_St10_St14cat_st10_25000bp_norm_ICE_autoCorr --BED ${BED} --mode ${MODE[1]} --range ${RANGE} --numberOfBins ${NUMBERofBINS} --transform ${TRAN[2]} --operationType ${OPTYPE[1]} --largeRegionsOperation ${LRO[0]} --outFilePrefixMatrix norm_smallest_esc_CyO_St10_St14cat_st10_25000bp_norm_ICE_autoCorr --outFileContactPairs ContactPairs --outFileObsExp FileObsExp --diagnosticHeatmapFile diagnosticHeatmapFile --chromosomes chr3R
The h5 resolution is 5000bp RANGE="300000:1000000" NUMBERofBINS=30
Here is the error I get:
I don't understand what is wrong,
Thanks for your help, Best, Tanguy