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Mismatch between gene IDs in Map-SeqNum-ID.txt and HierarchicalGroups.orthoxml

oma orthology pyham written 21 days ago by eschang1 • 10 • updated 21 days ago by adrian.altenhoff • 610

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OMA gene vs splicing variants in the output

orthologs oma orthologs oma pyham written 28 days ago by mateusz.konczal • 0 • updated 24 days ago by adrian.altenhoff • 610

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Pyham - pyham.taxonomy.Taxonomy object by constructing a ete3.Etree

hogs orthoxml pyham written 12 months ago by dtejadamartinez • 20 • updated 5 months ago by Christophe Dessimoz • 540

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Recent Replies

A: get GTEx mean expression by tissue by husensofteng • 70
You should use this file instead, it has the tissue names in the header: [Gene expression (TPM )...
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> bam file ?
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![enter image description here][1] ;-P [1]: https://image.ibb.co/dfsqrx/upvote_accept_bookma...
A: Convert physical positions from Hg18 to Hg19 by ATpoint ♦ 16k
You should convert this file to the [BED][1] format and then read and/or follow https://www.bio...
C: Estimating LD score in PLINK by GabrielMontenegro • 520
When I add the `--ld-window` parameter with the other commands, I get this message: `Error: Missi...
C: Tools To Calculate Average Coverage For A Bam File? by Michael Dondrup ♦ 46k
You might have incredibly high coverage :) I would try a different tool, now 8 years later. Hones...
C: Estimating LD score in PLINK by chrchang523 ♦ 5.0k
"9999999" should be fine; with more, you'd run out of disk space anyway.
C: RNA Seq, annotation, RNA Class by Bastien Hervé ♦ 4.2k
You can have a look at [BiomaRt][1] from Ensembl [1]: https://bioconductor.org/packages/relea...
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Hi! I used this R code with Rsamtools with my bam file and the result was: 6503.159 What coul...
C: Proovread terminated with error by prp291 • 50
Sorry. I used 17 million reads from a non-model plant. I have 70 GB with 8 threads.
C: Filtering Imputation output: how to filter on a VCF INFO field by rodd • 20
Thanks for this comment @Sunshine n Rain, it's nice and easy to filter out SNPs from vcf files ac...
C: Proovread terminated with error by ATpoint ♦ 16k
> How much memory is available, what is the organism and how many > threads have been used?...

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