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Hi!
I really like the way your tool works, and I was wondering if it was possible to use somehow your tool with bulk RNA-seq data (aligned with STAR) for HLA allele specific expression estimation.
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I've run alignment against a diploid transcriptome and used MMSeq to quantify expression on each of the two haplotypes for each transcript. How to calculate a p-value for allele specific expression (A…
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The current AIRR schema contains two `germline_database` keys, one in the `Alignment` another one in the `Rearrangement` object. However, this create a lot of redundancy, as usually all the `Rearrange…
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In the course of discussions reported in ticket #444 , we became aware that the current SO definition of “indel” (SO:1000032) is contrary to standard usage in our genetic research communities:
-Cur…
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Dear Stephane,
With great interest I have read your recent publication in Genome Biology and seen phASER, which I would really like to use for my own work. So I was wondering if I could ask your ad…
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Hello,
"Macromolecule biosynthetic process" concerning proteins and "production" of proteins are represented quite heterogeneously in the GO.
'GO:0009059 macromolecule biosynthetic process' has a …
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GO:0009626 plant-type hypersensitive response
The rapid, localized death of plant cells in response to invasion by a pathogen.
GO Comments
Note that term is to be used to annotate gene pro…
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Hi KB,
Attempting to run gbrs, followed the installation instructions here: https://churchill-lab.github.io/gbrs/
Getting the following conflicts:
```bash
$ conda create -n gbrs python=2
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As the Bowtie manual says, "--best --strata" does not apply for paired-end reads. What's the best solution to this? I really need to get only the best stratum.
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From discussion with Raymond:
The page can be a bit confusing for the user, especially if there are no afp papers for him/her. It would be easier to understand if we showed all the WormBase papers …