Moderator: Asaf

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Asaf6.5k
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Posts by Asaf

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Comment: C: Automating Workflow with multiple Inputs and Differing Variables
... 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 Asaf6.5k
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Comment: C: KEGG and metacyc database downloads
... No. You can try eggNOG-mapper to get KOs. Also what's the organism? ...
written 2 days ago by Asaf6.5k
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Comment: C: KEGG and metacyc database downloads
... EC and ko's are not 1:1 mapping ...
written 2 days ago by Asaf6.5k
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Answer: A: Venn diagram for ~12 shared SNP data
... You can try [UpSetR][1] to plot the interactions between the different groups. [1]: https://selenocysteine.github.io/rladies/ ...
written 2 days ago by Asaf6.5k
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Comment: C: cannot make BLAST database using makeblastdb command line tool
... My only advice is upgrade to 2.9.0 ...
written 5 days ago by Asaf6.5k
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Comment: C: cannot make BLAST database using makeblastdb command line tool
... Weird. Is it blast+ v 2.10.0 by any chance? ...
written 5 days ago by Asaf6.5k
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Comment: C: cannot make BLAST database using makeblastdb command line tool
... Are you sure you have all the chromosomes there? try `grep -c ">" custom_hg19.fa` ...
written 5 days ago by Asaf6.5k
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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 Asaf6.5k
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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 Asaf6.5k
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Answer: A: Best homology group in eggnog-mapper 2.0.1
... 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 Asaf6.5k

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