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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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problems with allhic #50

Closed mqding0564 closed 4 years ago

mqding0564 commented 4 years ago

Hi, I have got a problem when I was running the protocol. I have finished generating the sam file from fq1 and fq2 file, The generated sam file is about 100G, but when I was running the PreprocessSAMs.pl file, it doesn't report any mistake but give no results. The generated bam file is only 1.83K and also the data in sample.bwa_aln.REduced.paired_only.flagstat are zero. Can anybody help me resovle this problem. Thanks!

tangerzhang commented 4 years ago

Hi @mqding0564 Could you please post the command line you used? I assume that the restriction enzyme sites were mis-used.