Moderator: 5heikki
5heikki ♦ 8.6k
- Reputation:
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- Finland
- Last seen:
- 1 day, 1 hour ago
- Joined:
- 6 years, 2 months ago
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Posts by 5heikki
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... Calculate pairwise distances between the sequences and apply affinity propagation ...
written 3 days ago by
5heikki ♦ 8.6k
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154
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... This souds most plausible. Also, grep is probably the slowest/most inefficient possible way to do this.. ...
written 12 weeks ago by
5heikki ♦ 8.6k
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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 4 months ago by
5heikki ♦ 8.6k
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322
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1
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... Run the command in the directory where you actually have the files referred by the command? ...
written 4 months ago by
5heikki ♦ 8.6k
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138
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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") > "$F".column
done
Now in each dir you have a .column file an ...
written 4 months ago by
5heikki ♦ 8.6k
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290
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Comment:
C: Error when installing bedtools
... > I cannot upgrade gcc/g++ using sudo command because I am installing it on hpc cluster.
You can install your own gcc/g++ like any other program, can't you? Then you just direct make to use that one.. ...
written 4 months ago by
5heikki ♦ 8.6k
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4
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538
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Comment:
C: Python FASTA scripting
... This will fail with fasta files that have linebreaks in seqs, no? ...
written 4 months ago by
5heikki ♦ 8.6k
0
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1
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292
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... This will tell you how many percent of the reference genome your reads cover (or vice versa if you map ref reads on your assembly). Here reads are unpaired, so adapt to your needs where necessary..
bowtie2 \
-x "$GENOME" \
-U "$READS" \
--end-to-end \
--very-sens ...
written 4 months ago by
5heikki ♦ 8.6k
0
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1
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292
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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 4 months ago by
5heikki ♦ 8.6k
2
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1
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292
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1
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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 4 months ago by
5heikki ♦ 8.6k
Latest awards to 5heikki
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: NCBI API for finding accession numbers?
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?
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?
Appreciated
7 months ago,
created a post with more than 5 votes.
For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Appreciated
9 months ago,
created a post with more than 5 votes.
For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Appreciated
9 months ago,
created a post with more than 5 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
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?
Commentator
13 months ago,
created a comment with at least 3 up-votes.
For C: Finding a sequence in a fasta file
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?
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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