Moderator: 5heikki

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5heikki6.3k
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Posts by 5heikki

<prev • 912 results • page 1 of 92 • next >
5
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Answer: A: How can I redirect R's output from the console to a file
... sink("yourOutput.txt") your stuff sink() ...
written 12 days ago by 5heikki6.3k
3
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1
answer
83
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1
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Comment: C: Extract fasta sequences from main list using a list of titles
... https://www.biostars.org/p/49820/ https://www.biostars.org/p/77442/ https://www.biostars.org/p/1709/ etc. This question has been asked like at least 100 times. Did you search before posting? ...
written 13 days ago by 5heikki6.3k
0
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2
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Comment: C: Size Variation Of The 16S Gene
... I think such variation is completely normal. In e.g. [current RDP][1] (large file) the longest bacterial 16S rRNA is 2,487 bp. I imagine the majority of the length difference between that and the 1,541 bp reference E. coli 16S is due to hyper variable regions. If it's important, you could align a ra ...
written 19 days ago by 5heikki6.3k
0
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4
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187
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Comment: C: Split fasta to multi fasta
... It worked fine with OP's example data though ...
written 20 days ago by 5heikki6.3k
1
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4
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Comment: C: Split fasta to multi fasta
... This could work, but is not elegant at all sed 's/^>.*/N/' seqs.fa | awk 'BEGIN{RS="N";OFS="\n";i=1}{if(length($0)>1){print ">seq_"i,$0; i++}}' | grep . ...
written 20 days ago by 5heikki6.3k
0
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4
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187
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Comment: C: Split fasta to multi fasta
... Not just a little bug. It doesn't work at all. Lesson of the day: don't post answers while tired. ...
written 20 days ago by 5heikki6.3k
0
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4
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187
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Answer: A: Split fasta to multi fasta
... Original (fails with multifasta): awk 'BEGIN{RS="N"; OFS="\n"; i=1}{if(length($NF)>1){print ">seq_"i,$NF; i++}}' seq.fa New version (should work with everything): sed 's/^>.*/N/' seqs.fa | awk 'BEGIN{RS="N";OFS="\n";i=1}{if(length($0)>1){print ">seq_"i,$0; i++}}' | grep . ...
written 21 days ago by 5heikki6.3k
3
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1
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Comment: C: Append two fasta sequences
... Alternatively: `paste -d '' file1 file2 | sed 's/>/:/2'` or e.g. `paste -d '' file1 <(tr ">" ":" ...
written 27 days ago by 5heikki6.3k
1
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2
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Answer: A: Best reference database for 16S soil datasets?
... RDP and Silva are both fine. Silva is more restrictive in terms of its licence but it's fine for academic use.. ...
written 27 days ago by 5heikki6.3k
0
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1
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398
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Answer: A: Can I Use blastdb_aliastool and Accessions List Make a Bacteria Subset Nr Databa
... Here's a really impractical solution: #!/bin/bash mkdir all_prot cd all_prot wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt awk 'BEGIN{FS="\t"}{print $20}' assembly_summary.txt \ | awk 'BEGIN{OFS=FS="/"}{print "wget "$0,$NF"_protein.faa.gz" ...
written 27 days ago by 5heikki6.3k

Latest awards to 5heikki

Teacher 1 day 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?
Teacher 12 days 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 12 days ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Commentator 27 days ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Scholar 4 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 4 weeks 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?
Teacher 5 weeks 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 9 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Are old versions of NCBI's nr stored somewhere?
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: fasta header with leading zeros
Popular Question 3 months ago, created a question with more than 1,000 views. For Are old versions of NCBI's nr stored somewhere?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: fasta header with leading zeros
Scholar 4 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Common name to latin/scientific name converter
Teacher 5 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 5 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Student 5 months ago, asked a question with at least 3 up-votes. For Are old versions of NCBI's nr stored somewhere?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Teacher 7 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?

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