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Good day.
Thank you for this tool.
I have a few questions.
Can you please clarify the input/output requirements for RIBO-former a little better?
For example, I'm not sure if the fasta files s…
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I may be making the wrong assumptions but I noticed if I search for some of the nucleotide sequences in the pos_skipped_exon file in the pos_SE_transcripts file I am unable to find the inclusion of th…
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Hi,
Firstly, thanks for this great tool! It's going to be very helpful for my project.
I generated a novel transcriptome with Stringtie, and annotated it (i.e., 'named' each isoform) with GFFc…
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Dear Ángeles,
I am doing transcriptome study for the dog. I intend to look into differential gene expression and isoform usage between tissues and have got tappAS-compatible gff3 files by applying …
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I've been trying to run the "final test" with the human and mouse assembly to check my installation and it seems to fail somewhere in step 3, everything looks normal until that point:
````
#### ST…
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Hi FragPipers,
I am trying to do a basic analysis with the DIA_DIA-Umpire_SpecLib_Quant workflow, but I am running into trouble when I get to Spec Lib. When it is checked, I get an error as in the …
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Hello,
I'm using short reads with SQANTI QC, but my Illumina data is unstranded. Can SQANTI work with that, or does it require stranded short reads?
Also, if I have external RNA-seq can I use th…
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**Operating system**
Ubuntu 22.04.2 LTS (GNU/Linux 5.19.0-43-generic x86_64)
**Package name**
pigeon 1.2.0 (commit -v1.2.0)
**Conda environment**
[# packages in environment at /home/administr…
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To Whom It May Concern,
When trying to quantify isoform expression for a dataset (attached) by "**python $LIQA_PATH/LIQA.py -task quantify -refgene $refgene_PATH/chr1.refgene -bam $data_PATH/test1.…
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The mouse annotations seem to be for 2 lncRNA (although they all appear to be
for the same locs using different identifiers. I think some of these correspond to degradation products?
…