User: buchfink

gravatar for buchfink
buchfink140
Reputation:
140
Status:
Trusted
Location:
Last seen:
22 hours ago
Joined:
2 years, 7 months ago
Email:
b*******@gmail.com

Posts by buchfink

<prev • 11 results • page 1 of 2 • next >
4
votes
1
answer
154
views
1
answers
Answer: A: Diamond results non-specific compared to NCBI Web
... Diamond uses the LCA algorithm for taxonomic classification, which means that not only the top hit is used, but all hits within a 10% range of the best score. This can often lead to unspecific assignments. To get it more specific, use the `--top` parameter with a lower number, e.g. `--top 0` would o ...
written 11 weeks ago by buchfink140
0
votes
1
answer
1.4k
views
1
answers
Comment: C: diamond blastx always return error message "Insufficient arguments. Use diamond
... Try -a matches.m8. The version you are using is very old though, I recommend upgrading to the latest version. ...
written 9 months ago by buchfink140
0
votes
1
answer
1.4k
views
1
answers
Comment: C: diamond blastx always return error message "Insufficient arguments. Use diamond
... Please show us your command line and the full console output of Diamond. Also please run this and show us the output: diamond --version ...
written 9 months ago by buchfink140
1
vote
2
answers
342
views
2
answers
Answer: A: Why does some hits that show up in search against smaller database, but does not
... The evalue depends on the size of the database, so some hits might be above the evalue treshold (10) if you use the whole db. ...
written 11 months ago by buchfink140
1
vote
1
answer
677
views
1
answers
Comment: C: Long read alignment for MEGAN6
... Regarding your first question, I can't help you with that, please ask at the MEGAN community website (http://megan.informatik.uni-tuebingen.de/). DIAMOND does support long read alignment now, it has recently been implemented. ...
written 13 months ago by buchfink140
2
votes
1
answer
677
views
1
answers
Answer: A: Long read alignment for MEGAN6
... You can use DIAMOND (https://github.com/bbuchfink/diamond) for long read alignment. It now also supports frameshift alignments. Use the options -F 15 --range-culling. ...
written 13 months ago by buchfink140
1
vote
2
answers
915
views
2
answers
Comment: C: Blast duration time (+500 000 seqs)
... DIAMOND can do protein-protein alignment too, and it's much faster than BLAST. You should give it a try. ...
written 2.2 years ago by buchfink140
2
votes
1
answer
1.4k
views
1
answers
Answer: A: diamond blastx always return error message "Insufficient arguments. Use diamond
... Hi, the problem is that you're using a very old version of diamond which had a different syntax, and could only generate DAA files. I recommend upgrading to the latest version. ...
written 2.5 years ago by buchfink140
0
votes
4
answers
1.2k
views
4
answers
Answer: A: All vs. all pairwise sequence aligment
... You can try the DIAMOND aligner: https://github.com/bbuchfink/diamond ...
written 2.5 years ago by buchfink140
2
votes
2
answers
903
views
2
answers
Answer: A: Diamond sequence description
... You can use this command line option for showing the full subject title (more details are in the manual): `-f 6 qseqid stitle pident length mismatch gapopen qstart qend sstart send evalue bitscore` ...
written 2.5 years ago by buchfink140

Latest awards to buchfink

Scholar 11 weeks ago, created an answer that has been accepted. For A: Long read alignment for MEGAN6
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Diamond results non-specific compared to NCBI Web
Scholar 13 months ago, created an answer that has been accepted. For A: Long read alignment for MEGAN6

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1527 users visited in the last hour