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I'm wondering how possible it would be to create gene x cell matrices separated by strand in the case of stranded libraries. In other words, dropEst currently summarizes coverage over a given gene usi…
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A feature that I'd find very useful is parsing of gffutils GFF records into a (lightweight) Gene-like object. Something like:
```
# recs is a set of GFF records
gene_obj = make_gene_obj(recs)
# Acces…
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Hi,
I needed to parse the Pfam seed alignment. Because I needed to filter by **ID/ACC**, which is part of the **GF** set of features, I noticed that the per-file annotations are not saved. Since the …
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## Expected Behavior
I suppose that `tmp` directory should be automatically removed after normally running the `metaeuk`.
## Current Behavior
Now, Some `tmp` directory still exists and the resu…
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Hello,
I'm running STAR (STAR-2.7.9a) inside of a snakemake pipeline and it uses this command:
$STAR --genomeDir outputs/star_index --runThreadN 5 --readFilesIn outputs/reads/rrna_filtered/s1.1.fq…
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Hi, I am running Trinity v.2.9.1. in miniconda to assemble genome_guided transcriptome. After almost 18 hours I got this error message:
We are sorry, commands in file: [FailedCommands] failed. :-(…
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Hi, I ran rmats2sashimiplot with the code "nohup rmats2sashimiplot --b1 ./01.mapping/SNPL-F-1.bam,./01.mapping/SNPL-F-2.bam,./01.mapping/SNPL-F-3.bam --b2 ./01.mapping/QHZK-F-1.bam,./01.mapping/QHZK-F…
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Hi thanks for this great software. While using this I am unable to start with the continuous error of "Error reading fasta sequences - please check input files!". This error also occurring with test-s…
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**What is the SO term name and accession?**
SO:0001877 lncRNA
non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype.
**Describe what you …
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Hello,
I am running PsiCLASS on 43 RNA-Seq samples from Arabidopsis Thaliana. The whole run completes very fast and also produces quite good results. I compared the assemblies from PsiCLASS with th…