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Hello. This is Woo Jun Bang, and I'm trying to use this program for building orthograph reference data set!
I got this error when I wrote 'sh ortho_dl.sh culicidae 7157 0.9 0.9' for test.
Then I…
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Dear Authors,
OrthAgogue is a really useful software, specially in terms of its speed for
generating orthology relationships in large datasets. My compliments! I ran
OrthAgogue on a large datas…
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Hello,
I have a set of 100 UniRef proteins. I want to find orthologs of this set of proteins against a set of 44 transcriptomes. Would OrthoFinder help me in this ? I know OrthoFinder can find orthol…
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Steps to recreate bug:
1. Load a gene set (I used the default gene set.)
2. Add the Mouse mm9 to hg19 blastz genome comparison track
3. Load the find orthologs app. Load the gene set. Click Find or…
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I have the correct species tree for an analysis and I would want orthofinder to use it to detect orthologs; it possible to specify a tree for orthofinder?
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Hi there,
I've been scouring the documentation for how --onlyOrthologs works in hal2maf but haven't been able to figure it out. I'm working on identifying conserved sequences in a series of distant…
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Gene symbols (e.g. SSH) are a bit degenerate with respect to ortholog loci. This presents a couple of challenges for TKBIO:
1) The nature of the differences is not explicit in the UI, that is, two …
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Orthologs links seem to be broken in the gene view page, for instance, coming from:
https://wwwdev.ebi.ac.uk/gxa/sc/experiments/E-HCAD-4/results/gene-info?geneId=ENSG00000142937&markerGeneK=44&k=44…
pcm32 updated
4 years ago
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Hello,
I try to use your tool with two files containing cdna sequences, to determine pairwise Ks, Ka, and Ka/Ks values for orthologs (two distinct datasets). I blasted the XXX.cdna sequences vs the…
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Hi,
I'm trying to use aTRAM to select orthologs from reads of some WGS projects, but I'm having an time out error while running atram.py. Any idea what may be causing this?
Thanks in advance for y…