Moderator: 5heikki

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5heikki9.2k
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Posts by 5heikki

<prev • 1,240 results • page 1 of 124 • next >
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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 5heikki9.2k
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Comment: C: Compare elements between rows and columns
... 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 5heikki9.2k
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Answer: A: Compare elements between rows and columns
... 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 5heikki9.2k
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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 5heikki9.2k
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Answer: A: Modify query names longer than 252
... 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 5heikki9.2k
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Comment: C: blastn: -negative_taxids not working
... 561 is Escherichia (genus) 562 is Escherichia coli (species) ...
written 28 days ago by 5heikki9.2k
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Comment: C: Where can get processed metagenome datasets?
... Have a look at https://www.mg-rast.org/ ...
written 28 days ago by 5heikki9.2k
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Comment: C: blastn: -negative_taxids not working
... 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 5heikki9.2k
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Comment: C: blastn: -negative_taxids not working
... 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 5heikki9.2k
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Comment: C: blastn: -negative_taxids not working
... 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 5heikki9.2k

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Scholar 11 days ago, created an answer that has been accepted. For A: NCBI API for finding accession numbers?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For #saveNCBI - it's a joke, right?
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 7 months ago, created an answer that has been accepted. For A: NCBI API for finding accession numbers?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Popular Question 9 months ago, created a question with more than 1,000 views. For #saveNCBI - it's a joke, right?
Scholar 13 months ago, created an answer that has been accepted. For A: NCBI API for finding accession numbers?
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Scholar 15 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
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