Moderator: 5heikki
5heikki ♦ 9.2k
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Posts by 5heikki
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Comment:
C: Bacterial GWAS analysis
... I suggest that you spend more time describing your problem. What is your data? What have you done? What is the expected output? Etc. ...
written 10 hours ago by
5heikki ♦ 9.2k
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... Consider this mock file:
id1 60 up
id1 50 up
id1 40 down
id2 60 up
id2 90 down
id2 90 down
id3 70 up
id3 71 up
id3 90 down
I want the rows with the highest value from the 2nd column ...
written 11 days ago by
5heikki ♦ 9.2k
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... Perhaps:
sort -t $'\t' -k1,1 -k5,5gr inputFile | sort -t $'\t' -uk1,1 --merge
If it's a really large file you should also set `-S` `--parallel` and perhaps `-T`, see `man sort` ...
written 11 days ago by
5heikki ♦ 9.2k
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129
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Comment:
C: Greengenes OTU ID
... Just commenting that greengenes is dead as it hasn't been updated in nearly a decade. RDP and Silva provide much more up to date 16S reference data sets.. ...
written 27 days ago by
5heikki ♦ 9.2k
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120
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... How about
`zcat yourFile.fq.gz | paste - - - - | awk 'BEGIN{FS="\t";OFS="\n"}{print "@"NR,$2,$3,$4>new.fq;print NR"\t"$1>map}`'
Assuming there are no line breaks in the fastq seqs.. (I have never seen a fastq file with line breaks in seqs). Also, not tested and written on my phone from memor ...
written 28 days ago by
5heikki ♦ 9.2k
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... 561 is Escherichia (genus)
562 is Escherichia coli (species) ...
written 28 days ago by
5heikki ♦ 9.2k
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126
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... Have a look at https://www.mg-rast.org/ ...
written 28 days ago by
5heikki ♦ 9.2k
0
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145
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1
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... Overall the NCBI is awesome but their documentation is often rather.. well not awesome. I'm not saying this is for sure the solution to your problem, but it wouldn't surprise me at all if it was.. ...
written 29 days ago by
5heikki ♦ 9.2k
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... Yes, but it may be a special case. Doesn't hurt to try listing all the taxids under it and then giving blast that list as in the linked article.. ...
written 29 days ago by
5heikki ♦ 9.2k
0
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... Ok, actually the problem is (probably) the resolution of that taxid.
From [here][1]
> BLAST only accepts taxids that are at or below the species level.
A potential solution to your problem is in the linked article. You create a full list of taxids under the 562 taxid..
[1]: https://www.ncb ...
written 29 days ago by
5heikki ♦ 9.2k
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For C: Finding a sequence in a fasta file
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