Moderator: 5heikki

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5heikki8.6k
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Posts by 5heikki

<prev • 1,166 results • page 1 of 117 • next >
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Answer: A: sequence similarity analysis between groups of closely related DNA sequences
... Calculate pairwise distances between the sequences and apply affinity propagation ...
written 3 days ago by 5heikki8.6k
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Comment: C: grep with -f switch is not working
... This souds most plausible. Also, grep is probably the slowest/most inefficient possible way to do this.. ...
written 12 weeks ago by 5heikki8.6k
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Comment: C: Visualisation of clusters produced by mothur
... Correct me if I'm wrong, but your don't have any distance values in that file. Without such information, how would you go about doing hierarchical clustering.. ...
written 4 months ago by 5heikki8.6k
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Comment: C: awk, copy and paste single line command
... Run the command in the directory where you actually have the files referred by the command? ...
written 4 months ago by 5heikki8.6k
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Answer: A: Make a matrix from last coloumn of all files with different number of rows
... First you make a one column file with the gene names, then e.g.: for F in $(find . -maxdepth ? -type f -name "gene.tsv" | sort); do join -t $\t' -1 1 -2 ? -o 2.? -a 1 -e 0 geneNames.tsv <(sort -t $'\t' -k?,? "$F") > "$F".column done Now in each dir you have a .column file an ...
written 4 months ago by 5heikki8.6k
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Comment: C: Error when installing bedtools
... > I cannot upgrade gcc/g++ using sudo command because I am installing it on hpc cluster. You can install your own gcc/g++ like any other program, can't you? Then you just direct make to use that one.. ...
written 4 months ago by 5heikki8.6k
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Comment: C: Python FASTA scripting
... This will fail with fasta files that have linebreaks in seqs, no? ...
written 4 months ago by 5heikki8.6k
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Comment: C: How to determine which NCBI sequence to map against (multiple sequences for sing
... This will tell you how many percent of the reference genome your reads cover (or vice versa if you map ref reads on your assembly). Here reads are unpaired, so adapt to your needs where necessary.. bowtie2 \ -x "$GENOME" \ -U "$READS" \ --end-to-end \ --very-sens ...
written 4 months ago by 5heikki8.6k
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Comment: C: How to determine which NCBI sequence to map against (multiple sequences for sing
... What is "listed on NCBI" (your link) includes any DNA sequence from txid398626, not just genome assemblies. You can check "the best available" bacterial genome assemblies from ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt (I recommend that you don't open the link in browser ...
written 4 months ago by 5heikki8.6k
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Answer: A: How to determine which NCBI sequence to map against (multiple sequences for sing
... There's only one H. macacae genome in my slightly dated local RefSeq Bacteria copy: GCF_000507845.1 PRJNA224116 SAMN00690723 AZJI00000000.1 representative genome 1357400 398626 Helicobacter macacae MIT 99-5501 strain=MIT 99-5501 latest Scaffold Major Full 2013/12/13 Heli_maca_MIT_99-5501_V1 Br ...
written 4 months ago by 5heikki8.6k

Latest awards to 5heikki

Scholar 8 weeks ago, created an answer that has been accepted. For A: NCBI API for finding accession numbers?
Scholar 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 3 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
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
Scholar 4 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 5 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?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
Teacher 11 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?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Script for extracting data from a tab-delimited file
Scholar 11 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 11 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 11 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 11 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 12 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Scholar 13 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 14 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 14 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Popular Question 14 months ago, created a question with more than 1,000 views. For Print all rows that are in specified value range based on specific column as pairs

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