Activity for Dan Bolser
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Dan Bolser posted a comment on ticket #33
Thanks for looking at this Liubov. Are you actively using ATAC?
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To be honest, I don't know how to read the chain file format. It's possible it's incorrectly representing our 1-based database data.
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Hi Liguo, Thanks for getting back to me . The chain file I'm using is here: ftp://ftp.ensemblgenomes.org/pub/current/plants/assembly_chain/sorghum_bicolor/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain.gz Our internal (1-based) database has the following mapping: V2: 64231291 to 64603896 -> V3: 71417888 to 71790493 When I use our assembly converter tool (backed by crossmap) to 'see' this mapping using BED format, inputting this works: 1 64231291 64603896 but if I 'properly' 0-base the bed file:...
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To be honest, I don't know how to read the chain file format. It's possible it's incorrectly representing our 1-based data.
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Hi Liguo, Thanks for getting back to me . The chain file I'm using is here: ftp://ftp.ensemblgenomes.org/pub/current/plants/assembly_chain/sorghum_bicolor/Sorghum_bicolor_v2_to_Sorghum_bicolor_NCBIv3.chain.gz Our internal (1-based) database has the following mapping: V2: 64231291 to 64603896 -> V3: 71417888 to 71790493 When I use our assembly converter tool (backed by crossmap) to 'see' this mapping using BED format, inputtign this works: 1 64231291 64603896 but if I 'properly' 0-base the bed file:...
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BED off by one projection error.
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Mapping VCF over an inversion doesn't revcomp the alleles
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matchExtender: Assertion `0' failed
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A mere 18Tb free on that device, so I don't think that's the issue. Unfortunately,...
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Possible. I'll check.
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Uh?
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What's weird is that I've seen the -crossspecies mode run in other cases.
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What does seatac do?
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Is this still an issue? Can you explain the output of leaff --partitionmap and how...
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Error running ATAC in --crossspecies mode
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Putting the sequence 'all on one line' in the input fasta fixed the issue we were...
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Yeah, the 1-to-1 requirement is 'breaking' some of our alignments, so I'm trying...
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Ah, I remember this now. I thought the pipeline did this itself, but obviously not....
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Sorry, can't seem to edit to fix formatting...
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KeyError in DNA.DNA.reversecomplement()
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Thanks Brian, by space-based, do you mean zero offset? We aren't seeing this uniquely...
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From which tool?
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What should they do?
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Can you add more details here?
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Did this patch get merged?
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Can you submit a patch to fix this?
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Can I close this now?
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Alignments sometimes off by one?
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