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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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Hello,
Thank you for developing so nice package.
I tried to install ensembl-vep in my Ubuntu 18.04.2 local desktop computer.
It looks like I have something wrong with HTTP::Tiny. What I can d…
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### # Downloads input files:
### #Known variant file
`[wget ftp://ftp.ensembl.org/pub/release-99/variation/gvf/homo_sapiens/homo_sapiens-chr18.gvf.gz' -O homo_sapiens.vcf.gz](url)`
# # Select varia…
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Hi @smsrts,
Thanks for the updated ericscript.pl
I ran `ericscript.pl --printdb` and it's taking forever.
Output:
```
Selected Ensembl version: 1
Installed Ensembl version: No database i…
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hey, testing the package on Alexaki et al 2019 (human Ribo-seq)
Got an error I think is a bug, because I use a sparse bam file (2 Million reads only):
```
./RiboNT --gtf /media/roler/S/data/Bio…
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In https://github.com/related-sciences/ensembl-genes/pull/15, we use `bioregistry.normalize_curie` on the Ensembl provided cross-references for genes. Several of the prefixes used by Ensembl aren't su…
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Hi, im trying to generate a genome index with STAR and while the log shows no errors, half of the files are not there.
Under the same parameters other genomes run just fine.
Any help will be apprec…
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### Summary
A user wrote in to the forum regarding running FilterSamReads through GATK and the output bam file has formatting issues. After they sent in a bug report, I found that the exit code is g…
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After last two commits in recent days, I'm not able to successfully run `prepare_annotation_files` method (each of the updates introduced another error):
common initialization:
```
# to have all …
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bowtie2 -q -U unmapped.fastq -x /Drive1/find_circ/index/bow2_homo --reorder --mm --very-sensitive --score-min=C,-15,0 | /home/aclab/apps/find_circ/find_circ.py -G /home/aclab/homo.fa -p homo --stats …