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## Describe the issue
We continue digging into differences (https://github.com/Ensembl/ensembl-vep/issues/1031) caused by `--no_stats` workaround from https://github.com/Ensembl/ensembl-vep/issues/81…
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Hello there!
This is a very specific issue that that I wanted to try. So, it seems Trinity can't recover all full length transcripts for some specific genes (https://www.mdpi.com/2072-6651/10/6/249),…
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Hello,
I'm using EVidenceModeler (EVM) along with the following tools:
> Augustus
> Braker
Upon running EVM, I received results with a significantly lower number of genes than expected. When…
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Hi,
The transcript sequences that are output as the result of Isoquant are in the GTF format. These are essentially coordinates on the genome. I can then use gffread and genome fasta to extract the…
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Hi,
I used UCSC mm10 reference annotation as a guide to assemble transcripts (with -G mode on) from HISAT2 aligned reads, which I followed the same command (Step 3 assemble and quantify expressed g…
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Hello,
I would like to run factR2 on a custom assembly where I ran in the issue described in [https://github.com/f-hamidlab/factR2/issues/7](issue#7). So I thought I try it on the example data you …
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Hi there,
I read over the last thread from 2016 that dealt with this issue already, but I am using Stringtie 1.3.3b (which has an updated GFF parser since the bug from back then), and get the follo…
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Hello,
I found a few contradicting posts in bioinformatics forums whether Megahit could be used or must not be used for metatranscriptome assemblies from microbiome meta-RNA-seq data. I have it a …
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RefSeq transcript sequences can be different from the reference sequence (even if they agree with 1 build they can be different across builds). These sequences are aligned against the genome to produc…
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After quantification I tried simulating
IDs in expression profile:
NM_001001130.3
IDs in reference:
\>NM_001001130.3 Mus musculus zinc finger protein 85 (Zfp85), mRNA