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When aligning RNA-Seq reads simulated from transcripts extracted from genome+annotation, many (unsurprisingly) align to an incorrect splice-form. Basic, rnf-style evaluation focuses on the exact posit…
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Hi,
Recently I'm trying to use EVM to annotate my genome. Since I'm a freshman for gene structure annotation, I didn't get any alternative splicing events from the final GFF. I searched for the manua…
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The Ensembl Perl APIs are apparently not installed.
This affects all the Ensembl-depending tools :
- supported-organisms-ensembl
- perl-scripts/download-ensembl-features
- perl-scripts/downl…
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The annotation approach added in #282 seems to be working out pretty well, and I had a few thoughts about how to extend and/or regularize it, as well as how to evaluate it.
My major realization is …
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Dear all,
I am new user for DEPICT. I went through the DEPICT example script. It works well in my PC. However, I found some data is missing from the downloaded newest version package. If they are m…
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I am using jcvi in google colab.
It installs.
I am following this tutorial.
[Download data](https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)#download-data)
I run this command…
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Hi @tropfenameimer,
I need to create the mouse database with an additional motif.
In order to run create_cisTarget_databases the procedure say that you need the motif collection and the FASTA file.
…
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I am having this problem using the SAM file to identify the off-target
python ~/bin/guideseq-1.0.2/guideseq/guideseq.py identify --aligned ~/Desktop/WORKS/CODE/download/AA_1.sam --target_sequence c…
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I downloaded the latest version of starfusion singularity image
star-fusion.v1.11.1.simg
Then used the following command to generate a Rat novergicus library with the latest ensembl references a…
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+ Completeness (A1=both UTRs, A2=near-complete, B=most, C=something). ? @rchikhi QC + @taltman UTR annots?
+ Annotation of genes and other features (@taltman pipeline).
+ Find closest known full-len…