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Moderator: Asaf

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Asaf ♦ 8.1k
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Israel
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Posts by Asaf

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Comment: C: How to used extraction above 90% identity with blastp?
... Exactly, thanks for the references, I had a vague memory of this explanation. ...
written 1 day ago by Asaf ♦ 8.1k
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Answer: A: Comparing v3 and v4 datasets with v3-v4 amplicon datasets
... You have two issues here (at least) - one is how to align them and the other is to account for the amplification bias in each of the primer sets. Honestly, I don't see a way to merge the separate V3 and V4. If you'll chop the V3-V4 into separate V3 and V4 you will end up with low quality bases that ...
written 1 day ago by Asaf ♦ 8.1k
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Comment: C: How to used extraction above 90% identity with blastp?
... You're right although I've seen some cases in which this filtering failed, maybe they fixed it in the new version. ...
written 1 day ago by Asaf ♦ 8.1k
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Comment: C: Extracting Snps with pvalue <5x10-8 from gwas result
... Make sure you have such p-values. Maybe try with `$4<=0.01` ? ...
written 2 days ago by Asaf ♦ 8.1k
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Comment: C: -m option of HTSeq in featureCounts
... Are you sure you want HTSeq-count? There are better tools for evaluating transcript levels nowadays, if this is what you are indeed doing. ...
written 2 days ago by Asaf ♦ 8.1k
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Answer: C: Preparing files to call by Manta
... See Albert's point no 3 here: https://www.biostars.org/p/304614/ it's not secondary alignment, it's supplementary. In the example you gave, two parts of the read are mapped to different locations so both are primary but one is probably tagged as supplementary (bit 2048 as opposed to bit 256) ...
written 2 days ago by Asaf ♦ 8.1k
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Comment: C: Preparing files to call by Manta
... I think it has to do with the way the mapper keeps multi-mapping reads. Which mapper did you use? ...
written 2 days ago by Asaf ♦ 8.1k
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Comment: C: How to used extraction above 90% identity with blastp?
... I'm sorry, I couldn't understand you ...
written 2 days ago by Asaf ♦ 8.1k
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Answer: A: How to used extraction above 90% identity with blastp?
... The third column of your output file is the percent identity (`pident`), you can use awk to filter according to it: awk '$3>=90' outfile.fa And you would probably want to change the output file from `outfile.fa` to `outfile.txt` since it's not a fasta file. ...
written 2 days ago by Asaf ♦ 8.1k
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Comment: C: meaning of CheckM output
... Exactly. CheckM couldn't assign this genome into a lower level of taxonomy, potentially because it was contaminated with a bacterium from another phylum. ...
written 2 days ago by Asaf ♦ 8.1k

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