Moderator: 5heikki

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5heikki6.1k
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Posts by 5heikki

<prev • 902 results • page 1 of 91 • next >
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Answer: A: else condition in bash
... Your title should be else condition in awk, not bash. #!/bin/bash mkdir output not for i in $(find . -maxdepth 1 -type f -name "*.txt"); do awk -v O1="output/$i" -v O2="not/$i" \ '{if(($NF>70) && ($3>30)){print $1,$2,$3,$NF > O1} else{print $0 > O2}}' $i ...
written 1 day ago by 5heikki6.1k
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Answer: A: Whole genome assembly of Ion torrent single-end data
... [SPAdes][1] works best with bam files straight out of PMG. Good start would be: `--iontorrent -k 21,33,55,77,99,127 --careful` This generally results in ca. 100 contigs, which is pretty decent for bacterial genomes. You can't have much better than that with short reads. This is good enough for RefS ...
written 4 days ago by 5heikki6.1k
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Answer: A: how to remove rows based on certain characters
... sort -t $'\t' -k3,3 -k2,2gr file | sort -t $'\t' -u -k3,3 Also: `man sort` ...
written 5 days ago by 5heikki6.1k
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Comment: C: How to Install SGE (Sun Grid Engine) on macOS Sierra?
... Last update to [Son of Grid Engine][1] was 2016-03-02 [1]: https://arc.liv.ac.uk/trac/SGE/wiki ...
written 5 days ago by 5heikki6.1k
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Answer: A: what I want to do after the PhD?
... Start a company, sell it for billions (or at least 100s of millions) and retire before turning 40. ...
written 9 days ago by 5heikki6.1k
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Answer: A: Using Blast Command Line to output unaligned FASTA
... You can do e.g. this: blastp -db swissprot -query [FASTA_FILE] -evalue 0.005 -outfmt '6 sseqid sseq' \ | awk 'BEGIN{FS="\t"; OFS="\n"}{gsub(/-/, "", $2); print ">"$1,$2}' \ > homologs.fasta ...
written 9 days ago by 5heikki6.1k
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Comment: C: Align multiple gene clusters: mummer skips random sequences in multi fasta files
... MUMMER assumes that your query and reference files both represent single similar(ish) genomes. If you read through the manual, you'll e.g. find a section titled "Use cases and walk-throughs". It's all about complete/near complete genomic sequences, not fractions of multiple genomes. MUMMER is great ...
written 12 days ago by 5heikki6.1k
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Comment: C: Align multiple gene clusters: mummer skips random sequences in multi fasta files
... MUMMER is designed to find maximal matches between genomic sequences. Your input data sounds like something completely different.. ...
written 12 days ago by 5heikki6.1k
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Comment: C: Align multiple gene clusters: mummer skips random sequences in multi fasta files
... Wrong tool for the job. E.g. cd[-][1]hit would suit your needs far better.. [1]: https://github.com/weizhongli/cdhit ...
written 12 days ago by 5heikki6.1k
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Comment: C: uQ - small binary FASTQ
... What about just throwing​ away seqs with N's? How much information would really be lost vs. space saved? ...
written 15 days ago by 5heikki6.1k

Latest awards to 5heikki

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

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