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These seem to be CVMFS
Identified so far
* `dm3`
* [testing history](https://usegalaxy.eu/u/jenj/h/galaxy-workflow-galaxy-hi-c-1) using the [hic workflow in this tutorial](https://training.gala…
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bwa command line from GATK: `bwa mem -K 100000000 -p -v 3 -t 16 -Y $bash_ref_fasta`
bwa mem reference page: https://bio-bwa.sourceforge.net/bwa.shtml
What the options mean:
```
-K: minimum seed len…
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Is there anything similar in VG to the -C option in BWA MEM?
From the BWA mem manual
> -C Append append FASTA/Q comment to SAM output. This option can be used to transfer read meta information (…
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Hi author:
I am now using juicer to dealing my HI-C data, but when i run the script, i got an error, which is "invalid argument:mem --"5"". I opened the juicer.sh and found that in line 364, ther…
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Hi,
i am currently trying to figure out why my bwa-mem2 version 2.2.1 produces different (and pretty obviously bad) alignments from bwa mem (0.7.18).
I run both tools with -K 100000000000 -Y and…
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Ref workflow: https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/hicexplorer/workflows/
Ref IDC feedback: https://github.com/galaxyproject/idc/issues/53
Ref reported a…
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Hi:
Is the Canvas SmallPedigree-WGS applicable to bwa MEM bams ?
thanks.
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Only for required genome fasta / subset for HLA to make mapping much faster and less memory intensive.
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Hi all, I got an interesting and unexpected error.
Unfortunately, I can not retrieve the bam file to see what it is about:
```bash
samtools sort: failed to read header from "-"
```
the log:
```b…
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Dear Sir/Madam,
When I automaticaly generate test using "snakemake --generate-unit-tests" for the bwa_map rule below , the tests fails. The reason for the test failure is that it copies to the data d…