Moderator: 5heikki
5heikki ♦ 8.6k
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- Finland
- Last seen:
- 11 hours ago
- Joined:
- 5 years, 11 months ago
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Posts by 5heikki
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... 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
5heikki ♦ 8.6k
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... Run the command in the directory where you actually have the files referred by the command? ...
written 20 days ago by
5heikki ♦ 8.6k
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... 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") > "$F".column
done
Now in each dir you have a .column file an ...
written 5 weeks ago by
5heikki ♦ 8.6k
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Comment:
C: Error when installing bedtools
... > I cannot upgrade gcc/g++ using sudo command because I am installing it on hpc cluster.
You can install your own gcc/g++ like any other program, can't you? Then you just direct make to use that one.. ...
written 5 weeks ago by
5heikki ♦ 8.6k
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290
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4
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Comment:
C: Python FASTA scripting
... This will fail with fasta files that have linebreaks in seqs, no? ...
written 6 weeks ago by
5heikki ♦ 8.6k
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210
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... This will tell you how many percent of the reference genome your reads cover (or vice versa if you map ref reads on your assembly). Here reads are unpaired, so adapt to your needs where necessary..
bowtie2 \
-x "$GENOME" \
-U "$READS" \
--end-to-end \
--very-sens ...
written 6 weeks ago by
5heikki ♦ 8.6k
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... 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
5heikki ♦ 8.6k
2
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210
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... 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
5heikki ♦ 8.6k
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... Might be useful to provide exact commands used, exact errors reported by the program, etc. ...
written 8 weeks ago by
5heikki ♦ 8.6k
2
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142
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Comment:
C: databases in ncbi
... ftp://ftp.ncbi.nlm.nih.gov/blast/db/README ...
written 8 weeks ago by
5heikki ♦ 8.6k
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For C: Finding a sequence in a fasta file
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For A: How To Batch Grab All Ko (Kegg Ontology) Terms Associated With Each Kegg Pathway
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For A: Script for extracting data from a tab-delimited file
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For Print all rows that are in specified value range based on specific column as pairs
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