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Hi, skipper developer,
Thank you for developing skipper!
I have plotted two figures showing the peaks in the region of interest and the read depth of the CLIP data. In the area highlighted in Fi…
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Current loading procedure:
- load mRNA from fasta
- load peptide from fasta, link to mRNA via regexp
Problems with this strategy:
- we don't know locations of genes on scaffolds
- we can't prop…
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Running TRUST4 on 3' 10X genomics RNA-seq results in B cell inference where no B cells are present, any advice on fixing this issue?
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This is something I'd like to consider implementing, in the hopes that it would be used in one of the examples for the paper. It might not be necessary, but I do want to discuss it. @evancofer what do…
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I really love this tool and the output it gives, even for users like me.
From the RBP researcher point of view I have small suggestions:
- A normalization of overlaps like it is done in homer ( …
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Hi,
I'm using stringtie to assemble a transcriptome using a reference annotation made with a predict annotation containing only CDS regions.
This is the command line I'm using:
```
stringtie…
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Hello,
I have noticed that when running LOFTEE, the LoF_flags are not being properly annotated; they are always blank in the output. So, for instance, rs201677741 from the ExAC vcf is annotated by…
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I have the full Augustus annotations of a closely relates strain that had been trained through Braker using RNA-seq. Is it possible for me to use the output of that annotation as input for Augustus to…
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I tried to merge genes with overlapping regions using agat_sp_fix_overlaping_genes.pl but it failed because their CDSs don't overlap, is there any way to fix this? Thanks!
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## Prokaryotes
This entry was created as part of issue #866 by @erasche on 2016-02-11. I split the issue to address separately.
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[A] list of things I promised my PI I'd file as issues, that are m…