Moderator: Asaf
Asaf ♦ 6.5k
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Posts by Asaf
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... Well, the straightforward way is to write a pipeline and then execute it for each pair of files. Take a look at the leading frameworks: nextflow, wdl and snakemake ...
written 1 day ago by
Asaf ♦ 6.5k
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... No. You can try eggNOG-mapper to get KOs. Also what's the organism? ...
written 2 days ago by
Asaf ♦ 6.5k
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... EC and ko's are not 1:1 mapping ...
written 2 days ago by
Asaf ♦ 6.5k
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... You can try [UpSetR][1] to plot the interactions between the different groups.
[1]: https://selenocysteine.github.io/rladies/ ...
written 2 days ago by
Asaf ♦ 6.5k
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... My only advice is upgrade to 2.9.0 ...
written 5 days ago by
Asaf ♦ 6.5k
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... Weird. Is it blast+ v 2.10.0 by any chance? ...
written 5 days ago by
Asaf ♦ 6.5k
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... Are you sure you have all the chromosomes there? try `grep -c ">" custom_hg19.fa` ...
written 5 days ago by
Asaf ♦ 6.5k
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Comment:
C: GWAS in mixed populations
... Well, most of the phenotypes are not strictly caused by one SNP or even one gene. If the SNP is not very common it might be monomorphic in a population. ...
written 5 days ago by
Asaf ♦ 6.5k
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Comment:
C: GWAS in mixed populations
... Why? Do you suspect there is a one and only SNP causing the phenotype in all populations? ...
written 5 days ago by
Asaf ♦ 6.5k
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... Okay, so after doing some digging, indeed the hmmer option is dead in V2 and diamond should be used also for previous versions. The list of OGs contains orthology groups from different taxonomic levels, having the taxid after the "@" so in the example above `1UCFI@1239,COG2843@1,COG2843@2` means the ...
written 5 days ago by
Asaf ♦ 6.5k
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