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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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get a blank heatmap with ALLHiC_plot and bwa mem data #64

Closed Zachary-Wu closed 4 years ago

Zachary-Wu commented 4 years ago

Hi,

Thanks for sharing this amazing tool.

I am building the assemblies according to the homepage pipeline, and the bwa sampe is quite time-consuming,

so, at the same time, I tried to use the bwa mem data. everything looks good, but the heatmap is blank with a matplotlib user warning: "converting a masked element to nan", while I try to plot the heatmap.

I can't find a way to solve this matplotlib problem, Any help would be greatly appreciated.

Zachary-Wu commented 4 years ago

I find the reason.

it turns out that I renamed the Hic-reads to its $ac(accession number), so, "read_on_chr" just contains the information of one bwa-mam reads.

BY THE WAY, it is interesting that bwa mem may produce multiple mapped reads. so, I wonder if it may make more sense that we append an index at the end of read_id. Cause, in this case, all of the reads will be calculated in the "ALLHiC_plot" process.

tangerzhang commented 4 years ago

Hi @Zachary-Wu Glad you have solved this problem. For the bwa mem, you can extract uniquely mapped reads to avoid multiple alignments.