User: buchfink

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buchfink100
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Posts by buchfink

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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 8 weeks ago by buchfink100
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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 8 weeks ago by buchfink100
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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 4 months ago by buchfink100
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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 6 months ago by buchfink100
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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 6 months ago by buchfink100
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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 19 months ago by buchfink100
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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 23 months ago by buchfink100
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Answer: A: All vs. all pairwise sequence aligment
... You can try the DIAMOND aligner: https://github.com/bbuchfink/diamond ...
written 23 months ago by buchfink100
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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 23 months ago by buchfink100
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Answer: A: LAST/Poretools - where to start?
... You can try diamond (https://github.com/bbuchfink/diamond), it's a protein aligner similar to LAST but it has a native Windows version that does not require cygwin. ...
written 2.0 years ago by buchfink100

Latest awards to buchfink

Scholar 6 months ago, created an answer that has been accepted. For A: Long read alignment for MEGAN6

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