Michał T. Lorenc

Adding jbrowse visualization

4

### Description of feature Hi, I found [jbrowse pangenome visualization](https://github.com/pangenome/jbrowse-visualization) plugins. The good new is it requires the graph created by `pggb`. Additionally, it requires: - Generating MAF Files with...

Hi, I tried all different combinations to convert fast5 to fasta but none of them has converted it ``` > poretools fasta --type best 15 > poretools fasta --type best...

Hi, [Here](https://github.com/hillerlab/IterativeErrorCorrection/issues/2#issuecomment-248851522) is mention: > You should keep in mind that the fastq files will be converted to .fasta after the overlap correction (which, by default, is on) because the...

No module named flask.ext.wtf.SelectField

1

Hi, With latest dependencies versions, I got: ``` $ pip install flask flask-wtf wtforms $ pip install -e ./ $ python bin/runserver.py Traceback (most recent call last): File "bin/runserver.py", line...

Command web_search returned an error with docker

4

### ⚠️ Search for existing issues first ⚠️ - [X] I have searched the existing issues, and there is no existing issue for my problem ### Which Operating System are...

Hi, I ran `interproscan.sh --cpu 10 --input $1 --seqtype p --iprlookup --pathways --goterms -d $2 --tempdir interproscan-dp-tmp` and got the following output files: - augustus.hints_utr.aa.gff3 - augustus.hints_utr.aa.tsv - augustus.hints_utr.aa.xml Now...

Hi, Is it possible to use a self-created gff3 file for sleuth rather than to use ensembl via [biomarRt](https://github.com/cbcrg/kallisto-nf/blob/master/bin/sleuth.R#L19) for a de-novo project? Thank you in advance Michal

usage questions

4

HI, I am working on a hybrid assembly for a 3.2G allotetraploid plant genome: 1. Illumina assembly with [w2rap-contigger](https://github.com/bioinfologics/w2rap-contigger). 2. [DBG2OLC](https://github.com/yechengxi/DBG2OLC) to combine Illumina assembly with PacBio reads 3. [PBjelly](https://github.com/alvaralmstedt/Tutorials/wiki/Gap-closing-with-PBJelly)...

PBSpro support

7

Hi, Our HPC uses PBSpro. Does `make_lastz_chains` support PBSpro? Best wishes, MIchal

Adding more RNA-Seq predictions

1

### Description of feature Hi, I recently came across Mikado which is a pipeline to identify the most useful or “best” set of transcripts from multiple transcript assemblies. Our approach...