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mRNA with Short introns (
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I am receiving the following error as : IndexErro: list index out of range" though I used blast_out put file using SWissProt protein database, SwissProt protein database: uniprot_sprot.fasta. Command …
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[13:34:17] ERROR - File parsing failed, exiting...
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/share/apps/miniconda/anaconda3-2019.10/lib/python3.7/multip…
yye88 updated
2 years ago
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I do not entirely understand what is happening, but in some cases CDSs with ribosomal slippage from NCBI cause `double free or corruption (!prev)`:
```
$ gffread --version
0.12.7
$ curl https://…
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Hello,
Even with -overlap 0.0, Liftoff can generate overlapping exons (example : exon1 [400279 400378] exon2 [400378 400725])
How to avoid this ? Would it be possible to merge this kind of exons…
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**Describe the bug**
`agat_convert_sp_gff2gtf.pl` removes URL escape characters in the 9th column. In my testing, it removed a URL escape character in the 9th column which encodes for semicolons, i.e…
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Hi,
Your software seems perfect for generating an annotation file I need for a manuscript I'm working on. However, I'm having an issue with it:
I have a gtf file with the following features, CD…
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For input:
1. I have got a GFF file from PlasmoDB. "PlasmoDB-66_PvivaxP01.gff"
2. I converted it to GTF file using agat `agat_convert_sp_gff2gtf.pl --gff ../PlasmoDB-66_PvivaxP01.gff -o PlasmoDB-66_…
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I ran the Fix_start_stop on my genome but it does not resolve all
Total sequence length 496122366
Number of genes 19350
Number of mRNAs …
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Hi,
This is not a technical issue but a conceptual question.
Till date, I have been using HOMER for ChIP-seq and ATAC-seq peak annotation. As I intend to perform TOBIAS DNA foot printing analys…