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In the _Datasets_ section, it is stated that we use b37 in NEXT Bioinformatics, but at MOMA we use hg19. Unfortunately, while the two are very similar, that are [not 100% identical](http://gatkforums.…
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```
### Pipeline run code and environment:
* Command: `/my/path/pepatac/pipelines/pepatac.py -O /my/path/OUTPUT -P 10 --sample-name sample_S1_R1_001 --input /my/path/FastQ/sample_S1_…
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It would be great to have an (optional) module in the pipeline that generates coverage data for species of interest (e.g., all human infecting pathogens with greater than X number of hits).
Ideall…
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Hey! I am planning to use TRUST4 in order to extract TCR sequences from bulk whole mRNA seq (single end). I am puzzled about what reference sequence to use for this. Since I would like to evaluate clo…
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I think your objective is clear, but I have some confusion about the execution.
You mention that you intend on visualizing your alignments with `progressiveMauve`. Despite the problems associated w…
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Hi There,
Thank you for developing the PDR. I have a general question in regard to reference and assembly genomes. Reasonably, the new draft of assembly should be more complete or even larger (size) …
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Dear Felix,
Thank you so much for developing this great tool! I rely Bismark heavily for my research :)
Recently we developed a haplotype-resolved diploid human genome, where one copy is paterna…
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Hi,
Thanks for developing this nice tool.
I have two genomes, assembly1 and assembly2. My goal is to use these two genomes as reference genomes, align reads to each of them, and call variants. T…
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I was trying to use fastq_screen with --aligner "minimap2".
I encountered the error:
`Skipping DATABASE 'genome_xyz' since no minimap2 index was found at '/home/references/genome_xyz/genome_xyz.fa…
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> *[Filament](https://en.wikipedia.org/wiki/Galaxy_filament)* – A large-scale structure in the universe, consisting of a network of galaxies and galaxy clusters interconnected by dark matter and gas. …