Moderator: 5heikki

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5heikki8.6k
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Posts by 5heikki

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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 20 days 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 20 days 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") > "$F".column done Now in each dir you have a .column file an ...
written 5 weeks ago by 5heikki8.6k
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Comment: C: Error when installing bedtools
... > I cannot upgrade gcc/g++ using sudo command because I am installing it on hpc cluster. You can install your own gcc/g++ like any other program, can't you? Then you just direct make to use that one.. ...
written 5 weeks ago by 5heikki8.6k
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Comment: C: Python FASTA scripting
... This will fail with fasta files that have linebreaks in seqs, no? ...
written 6 weeks ago by 5heikki8.6k
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Comment: C: How to determine which NCBI sequence to map against (multiple sequences for sing
... This will tell you how many percent of the reference genome your reads cover (or vice versa if you map ref reads on your assembly). Here reads are unpaired, so adapt to your needs where necessary.. bowtie2 \ -x "$GENOME" \ -U "$READS" \ --end-to-end \ --very-sens ...
written 6 weeks 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 6 weeks 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 6 weeks ago by 5heikki8.6k
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Comment: C: Mira assembler has stopped working
... Might be useful to provide exact commands used, exact errors reported by the program, etc. ...
written 8 weeks ago by 5heikki8.6k
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Comment: C: databases in ncbi
... ftp://ftp.ncbi.nlm.nih.gov/blast/db/README ...
written 8 weeks ago by 5heikki8.6k

Latest awards to 5heikki

Scholar 12 days ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 27 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 28 days ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 6 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
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?
Good Answer 6 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 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 7 months ago, created an answer that was upvoted at least 5 times. For A: Script for extracting data from a tab-delimited file
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?
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
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Scholar 10 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
Popular Question 11 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
Teacher 12 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 12 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan

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