Moderator: 5heikki
5heikki ♦ 7.2k
- Reputation:
- 7,150
- Status:
- Trusted
- Location:
- Finland
- Last seen:
- an hour ago
- Joined:
- 4 years, 4 months ago
- Email:
- h***************@gmail.com
about me
Posts by 5heikki
<prev
• 1,006 results •
page 1 of 101 •
next >
1
vote
0
answers
80
views
0
answers
Comment:
C: BLAST in Linux - SOCK_SetupSSL
... My guess is that your Linux has tblastx in $PATH, however, it's so old that it doesn't support https.
You can verify with `tblastx -version`
The actual tblastx of blast 2.7.1 should be in ~/Documents/ncbi-blast-2.7.1+/bin/ and thus the call would be `~/Documents/ncbi-blast-2.7.1+/bin/tblastx -db ...
written 18 days ago by
5heikki ♦ 7.2k
0
votes
2
answers
189
views
2
answers
Answer:
A: Judging best assembly
... If there's a closely related genome available, why aren't you doing a reference guided assembly? Also, it might be a good idea to try different assemblers. As to your two assemblies, they're essentially same except the bigger one includes more short contigs that may or may not be "good". I would go ...
written 19 days ago by
5heikki ♦ 7.2k
0
votes
2
answers
208
views
2
answers
... But then you might download representative over reference or vice versa randomly (depending how the file is sorted). Of course that might not matter. You could sort the assembly summary file first based on that column. At least then it would be consistent for sure.. ...
written 24 days ago by
5heikki ♦ 7.2k
0
votes
2
answers
208
views
2
answers
... In those two cases the first match has "representative genome" in the fifth column. I don't know if NCBI has ordered the file that way. Perhaps it would be wiser to filter for that if "reference genome" fails. Then if you still get empty query you can take the first match or alternatively look into ...
written 24 days ago by
5heikki ♦ 7.2k
3
votes
2
answers
208
views
2
answers
... #!/bin/bash
TAXID="$1"
if [[ -z "$TAXID" ]]; then
echo "Usage: retrieveReference.sh NcbiTaxId"
exit
else
if [[ ! -e assembly_summary_genbank.txt ]]; then
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt
fi
...
written 24 days ago by
5heikki ♦ 7.2k
0
votes
1
answer
119
views
1
answers
... How could you get GG ID's with de novo OTU picking since reference is never used? You're picking OTUs de novo. And yes, you would have to use closed or open reference OTU picking to get the identifiers. Alternatively, I imagine you can somehow assign IDs to your de novo OTUs post OTU picking. ...
written 25 days ago by
5heikki ♦ 7.2k
0
votes
1
answer
202
views
1
answers
... Check from `blastn -help` output how to add a field to outfmt for sequence similarity and filter also based on that in the `awk` command. In case the "temp" file is still huge, you must have a lot of redundancy in your input. ...
written 4 weeks ago by
5heikki ♦ 7.2k
0
votes
1
answer
202
views
1
answers
... If the sequences are really short add `-task blastn-short` to the command. Also, is it possible that you don't have any "universal" seqs? ...
written 4 weeks ago by
5heikki ♦ 7.2k
1
vote
1
answer
202
views
1
answers
... This assumes that 1) blast is installed and that 2) the script is run in the dir where .fasta named files reside
#!/bin/bash
FILES=($(find . -maxdepth 1 -type f -name "*.fasta"))
for((i=0;i<${#FILES[@]}-1;i++)); do
blastn -query ${FILES[$i]} -subject ${FILES[$i+1]} -outfmt '6 ...
written 4 weeks ago by
5heikki ♦ 7.2k
0
votes
3
answers
184
views
3
answers
Comment:
C: using parallel program
... If your data is in format:
arg1arg2
arg1arg2
You should actually change the tabs to newlines before piping to parallel, e.g.
cat fna.ls | tr "\t" "\n" | parallel ...
The script was written for data that was in format like below:
arg1
arg2
arg1
arg2 ...
written 4 weeks ago by
5heikki ♦ 7.2k
Latest awards to 5heikki
Teacher
12 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?
Teacher
24 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?
Oracle
4 weeks ago,
created more than 1,000 posts (questions + answers + comments).
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?
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
5 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
5 months ago,
created an answer that has been accepted.
For A: The best way to share scientific findings with community
Great Question
6 months ago,
created a question with more than 5,000 views.
For Best tools for circular genome visualization?
Scholar
6 months ago,
created an answer that has been accepted.
For A: The best way to share scientific findings with community
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?
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?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Bootsrapped tree from a distance matrix
Good Answer
8 months ago,
created an answer that was upvoted at least 5 times.
For A: fasta header with leading zeros
Teacher
9 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?
Teacher
10 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?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1837 users visited in the last hour