Moderator: 5heikki

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5heikki7.0k
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Posts by 5heikki

<prev • 990 results • page 1 of 99 • next >
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Comment: C: Unsupervised Hierarchical Cluster Heatmap
... That's a good post. It's missing the top clustering algorithm though, i.e. [Affinity Propagation Clustering][1] [1]: https://cran.r-project.org/web/packages/apcluster/vignettes/apcluster.pdf ...
written 20 days ago by 5heikki7.0k
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Answer: A: Could not find a version of the library!
... On CentOS 7 `yum install boost-program-options` would solve this problem.. ...
written 26 days ago by 5heikki7.0k
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Answer: A: Find the same repeat sequence in two fasta files
... Do we have to do it in perl? blastn -task blastn-short -query file1 -subject file2 -outfmt '6 qseqid sseqid qlen slen length nident' | awk 'BEGIN{OFS=FS="\t"}{if($3==$4 && $3==$5 && $3==$6){print $1,$2}}' ...
written 27 days ago by 5heikki7.0k
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Comment: C: How to retrieve all pentamer from a sequence?
... That's nice to hear. Be sure to read the manual so you know what a canonical k-mer is. Or just see [here][1] [1]: https://www.biostars.org/p/153170/ ...
written 5 weeks ago by 5heikki7.0k
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Answer: A: How to retrieve all pentamer from a sequence?
... You can do this with e.g. [Jellyfish][1] [1]: http://www.genome.umd.edu/jellyfish.html ...
written 5 weeks ago by 5heikki7.0k
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Answer: A: Filtering out incorrect index combinations in fastq file
... I'm not sure if I understood correctly: awk 'NR%4==2{print substr($0,1,14)}' file.fq | paste - - | sort | uniq -c ...
written 5 weeks ago by 5heikki7.0k
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Comment: C: segmentation fault (core dumped) error when using BWA and BOWTIE
... My guess would be that OP is running out of RAM.. ...
written 5 weeks ago by 5heikki7.0k
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Comment: C: Comparing hierarchical clusterings
... Try [apcluster][1], I can almost promise to you that no matter the data, it will give you the best results. I'm quite surprised that it hasn't become de facto standard in all things bioinfo.. [1]: https://cran.r-project.org/web/packages/apcluster/index.html ...
written 8 weeks ago by 5heikki7.0k
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Comment: C: Finding fasta files that share the highest number of identical headers
... #!/bin/bash FILES=($(find . -maxdepth 1 -name "*.fa")) for ((i=0; i<${#FILES[@]}; i++)); do for ((j=0; j<${#FILES[@]}; j++)); do SCOUNT=$(comm -1 -2 <(grep "^>" ${FILES[$i]} | sort) <(grep "^>" ${FILES[$j]} | sort) | wc -l) echo -e "${FIL ...
written 8 weeks ago by 5heikki7.0k
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Answer: A: Finding fasta files that share the highest number of identical headers
... This is definitely not the most efficient way.. #!/bin/bash FILES=($(find . -maxdepth 1 -name "*.fa")) for ((i=0; i<${#FILES[@]}; i++)); do for ((j=0; j<${#FILES[@]}; j++)); do echo -e "${FILES[$i]}\t${FILES[$j]}" comm -1 -2 \ <(g ...
written 8 weeks ago by 5heikki7.0k

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Scholar 5 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
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Teacher 8 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?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Teacher 3 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 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
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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
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Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: fasta header with leading zeros
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?
Scholar 7 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
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 8 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 8 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 8 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
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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