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I encountered the following error when I test example data. Is there any solution to this error? Thanks.
[PEM-Q] primerChrom: chr15
[PEM-Q] primer_start: 61986633
[PEM-Q] primer_end: 61986652
[P…
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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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Hello,
If I understand correctly, FastQ-Screen checks for the existence of a BWA index by looking for the extension ".amb", ex. [here](https://github.com/StevenWingett/FastQ-Screen/blob/b9d0ebc4926…
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Either remove that genome from the list, or correct the dbkey in the data tables. It is probably truncated in one of the columns.
If selected, STAR indexes are "not found". Might have problems wit…
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### Describe the bug
Not sure from the log file what caused this or how to run it again manually. Log file attached, so hopefully that give you enough info to figure out what's going on.
### Is this…
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Hello!
I'm trying to run this:
`snippy --outdir GPSC33 --R1 ERR3261191_1.fastq.gz --R2 ERR3261191_2.fastq.gz --ref Reference_sequence_GPSC33.fa`
but I got this error:
`### samtools faidx r…
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Hello Xiaofei,
I have used HapHic at MAPQ1 NM < 3 as explained in the front matter page, the initial contigs were from the p_utg.fa and the --gfa file used was the corresponding gfa file.
.
By default,…
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Map sequences with bwa and use paired-end mode (documentation says it's fine). Then use pairtools to convert the pairs into coordinates (.pairs) to be loaded as a *cooler*.