Moderator: 5heikki

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5heikki6.3k
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Posts by 5heikki

<prev • 917 results • page 1 of 92 • next >
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Comment: C: blastn for very short sequences
... How about using e.g. Bowtie2 instead of blast? ...
written 11 days ago by 5heikki6.3k
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Answer: A: Modifying Standalone BLAST output
... You have to setup [taxdb][1] but with env_nt I think all the sequences are basically annotated as "Environmental sample" so not much will be gained.. [1]: https://www.ncbi.nlm.nih.gov/books/NBK279680/ ...
written 16 days ago by 5heikki6.3k
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Comment: C: How to repeat a row for each value of its corresponding column
... awk 'BEGIN{OFS=FS="\t"}NR==1{print $1,$2}NR>1{for(i=2;i<=NF;i++)print $1,$i}' file ...
written 17 days ago by 5heikki6.3k
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Answer: A: How to repeat a row for each value of its corresponding column
... awk 'BEGIN{OFS=FS="\t"}{for(i=2;i<=NF;i++)print $1,$i}' fileWoutHeader ...
written 17 days ago by 5heikki6.3k
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Comment: C: Clustering by sequence alignments
... Starting with distance matrices, [affinity propagation clustering][1] has worked quite nicely for me. [1]: https://cran.r-project.org/web/packages/apcluster/index.html ...
written 29 days ago by 5heikki6.3k
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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 6 weeks ago by 5heikki6.3k
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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 6 weeks ago by 5heikki6.3k
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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 7 weeks ago by 5heikki6.3k
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Comment: C: Split fasta to multi fasta
... It worked fine with OP's example data though ...
written 7 weeks ago by 5heikki6.3k
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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 7 weeks ago by 5heikki6.3k

Latest awards to 5heikki

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 6 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 6 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Scholar 9 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 9 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 10 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 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Popular Question 3 months ago, created a question with more than 1,000 views. For Are old versions of NCBI's nr stored somewhere?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: fasta header with leading zeros
Popular Question 4 months ago, created a question with more than 1,000 views. For Are old versions of NCBI's nr stored somewhere?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: fasta header with leading zeros
Scholar 5 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Common name to latin/scientific name converter
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 6 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Student 6 months ago, asked a question with at least 3 up-votes. For Are old versions of NCBI's nr stored somewhere?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Teacher 8 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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