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Hi Laura,
It would be great if there was an option to be able to submit a MSA instead of a protein sequence as input for gget alphafold. The use case here is to submit (manually) curated MSA, instead…
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I am wondering if DIA-NN uses only peptides that are unique to their assigned group for quantification of that group? For example, we are working with data from muscle where myosin heavy isoforms have…
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- (mostly . . . allow exons to overlap), just for specific isoforms
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as @cmdcolin noted, we have a bunch of code for frameshifts and they are in the code, but we do not appear to act…
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**Are you using the latest release?**
Hello Sir,
I am using funannotate 1.8.7 with the below command, but get an error of "the database is locked". Some issues suggested setting --CPU=1 or -T 1. Whe…
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Hi @srbehera
I wanted to try out your tool for clustering isoforms.
Unfortunately I get this error when I try to compile your code.
g++: error: ./edlib/edlib/src/edlib.cpp: No such file or direc…
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I am running STAR and StringTie on RNAseq data from 4 samples (PE 100bp, 60M reads/sample, stranded) and am looking at the merged.stats file. The numbers for novel stuff being found in my samples is R…
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Hi andr-kun,
I am trying to replicate your script manuscript/bash_files/TE_isoform_filter/transposon_isoforms_filter_hipsci.sh but I am having trouble finding the file GRCh38_nestedRepeats_20200703…
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Hey guys, thanks for the tool! Very useful!
I'm a bit confused about the "num_reps" parameter. And also who it relates to the event probabilities.
I have implemented an alternative splicing (AS)…
ls233 updated
7 months ago
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Since 17/Nov/2015, there were a few updates:
"You can see the list of changes below. Every attribute is preceded by a
symbol which is either + (addition), - (removal) or ~ (modification)."
**14…
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when I use the following command, I only get 0 values for the new pme columns in my isoforms.results. Input data is a single cell dataset. How can this be?
rsem-calculate-expression --paired-end --…