Hello,
Here is a link to some documentation from a Tool Shed's version of the
tool (don't worry to much about the particular repository or version,
this is just a particularly nice document):
http://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=860f5cf73e01ebca&tool_config=database/community_files/000/repo_240/tools/ncbi_blast_plus/blastxml_to_tabular.xml&changeset_revision=45ba7c750bc8
"qframe" is the 'query frame' - this is not the same as coverage.
How to calculate coverage is up to you and may not be simple if you have
overlapping HSPs. However, the basic concept is: total unique query
bases included in any HSP/total query length is common. You will find
with a quick web search that many people end up writing their own parser
(directly from the alignment, not the tabular output) to get to this
exact information, calculated in the way that they want it.
Best,
Jen
Galaxy team
On 2/3/14 11:20 AM, Deepak Datta wrote:
Hello,
I was working with _NCBI BLAST + blastx._. I have a question regarding
one of the columns that reads 'qframe'.
When we do Blast on NCBI, we get a column called query coverage. And
when we perform NCBI BLAST + blastx, we get 25 columns. I wanted to
know which of these columns is analogous to the "query coverage"
column. And if these columns do not correspond to "query coverage"
then can you kindly let me know how am I supposed to derive that?
Looking forward to your response.
--
/DD/
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Jennifer Hillman-Jackson
http://galaxyproject.org
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