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NCBI-Hackathons / EndoVir

Discovery of Novel Endogenous Viruses
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makeblastdb: local database and sequence retrieval ruckus #3

Closed janpb closed 7 years ago

janpb commented 7 years ago

Creating a local database using makeblastdb without Fasta ID [0] results in unusable names for subsequent retrieval. Testing two options:

  1. Format the input sequences using >ref|Accsession|name
  2. Testing different blastdbcmd -outfmt options

References

0 https://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_demo/#ch_demo.T5

DCGenomics commented 7 years ago

Try -parseseqids

On Oct 24, 2017 3:50 PM, "janpb" notifications@github.com wrote:

Creating a local database using makeblastdb without Fasta ID [0] results in unusable names for subsequent retrieval. Testing two options:

  1. Format the input sequences using >ref|Accsession|name
  2. Testing different blastdbcmd -outfmt options

References

0 https://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_demo/#ch_demo.T5 https://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_demo/#ch_demo.T5

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boratyng commented 7 years ago

It is -parse_seqids

janpb commented 7 years ago

Fixed. Thanks.