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I was just wondering if anyone knew which GTF file I should be using for my AS analysis.
I'm using mapped BAM files that I've aligned to a Glycine max reference genome.
However, If I'm doing alterna…
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The `to_diff()` function is great for showing differences between exons, but sometimes it is very useful to highlight differences between introns and individual splice sites.
Not sure if it wouldn'…
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* spladder version:
* Python version:3.6
* Operating System:
Operating System: Red Hat Enterprise Linux Server 7.2 (Maipo)
### Description
I tried to run spladder viz command
### What …
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Hello, I am trying this program. My commands are as follows:
galba.pl --genome=${genome_file} --prot_seq=${protein_file} --threads 40
My error is as follows:
ERROR in file ~/software/GALBA/scrip…
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I am working with sequencing data that has short insert sizes but was sequenced with 150 bp paired-end reads, leading to high levels of overlaps within the read pairs. When I visualized the data align…
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Hi,
I read your explanation about "--chunk-size" in Github issue, "Parameters for max reads and chunk size #68" You explained "Max chunk also just changes the size of the anchor window." (The o…
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I'm trying to annotate a protein with its genomic coordinates using transvar and for most proteins it works fine, but sometimes nothing is returned except for the header of the output. How should I in…
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Hi,
I am getting an error with the ProtHint step and I'm not sure what the cause of it is. Could it be because it couldn't find enough memory or something?
`error: ProtHint exited due to an err…
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Hello,
I have been unable to complete my ExOrthist run because of the following error:
ERROR : Unknown image format/type: /nfs/users/lserrano/lciampi/JuanRamon/Orthologies/ExOrthist/singularity…
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Hi,
I have not actually used chanjo for coverage reports but as I recall it provides reports of "completeness" on transcript or gene level.
Storing coverage data is tricky business since inclus…