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I tried running MUM&Co on several query-reference pairs. In several occasions, I got the error:
> Matching query and reference chromosomes
>
> awk: cmd. line:1: fatal: division by zero attempted…
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(Copied from the lastz mailing list)
we have run lastz version 1.04.15 with --queryhsplimit=keep,nowarn:200 on two softmasked mammalian genomes. The masking comes from repeatMasker. The reason for …
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Hi,
I was doing some tests using finder for a large plant genome.
At the end of alignments steps, a *.sortedByCoord.out.sam* and a *_for_psiclass.sam* are created and removed only at the end of th…
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Hello,
I am trying to run vg deconstruct on a vg file that I created from whole genome alignments. However, the command did not generate any output. None of the subcommands worked for deconstruct (…
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I mapped whole genome sequencing data using the `-a` option. Some alignments have a Flag total of 377 and 441. According to Explain SAM Flags internet tool, 377 includes mate unmapped, read reverse s…
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Dear author, multiz is a very useful software. However, at present, I need to merge more genomes, according to the pairwise merger speed is too slow, is there any way to improve the merger speed? Than…
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We should think about what our goals are, and make sure that we are providing something that isnt already available through projects such as biopython or scikit-bio.
Here are my specific needs:
…
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The whole genome pipelines now contains two main functional domains:
1) merging alignments and QC
2) variant calling
Given that 2) is already pretty complex and 1) is going to become more co…
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As we use splice aware aligner "Hisat2" to align our reads based on whole genome or even with specific chromosome (15) we found that the overall alignment of all reads approximately 5% .
This low ali…
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Hi Glenn!
I'm currently running `cactus-hal2maf` on a new alignment I've generated using Cactus v2.8.2. I'm running Cactus as a singularity image on a computing cluster. Anyways, I have an alignmen…