mkatari-bioinformatics-august-2013-blastnotes
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mkatari-bioinformatics-august-2013-blastnotes [2014/07/11 08:53] – mkatari | mkatari-bioinformatics-august-2013-blastnotes [2014/10/23 19:58] – mkatari | ||
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[[mkatari-bioinformatics-august-2013|Back to Manny' | [[mkatari-bioinformatics-august-2013|Back to Manny' | ||
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+ | This page contains a short introduction on how to create a Blast database and also how to run Blast using a query. Please replace your sequences with the names provided for the scripts to work for you. | ||
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+ | **Please remember** --- if you are planning to run Blast on command line, please do it in **interactive** mode. The recommended approach is to use sbatch scripts (described in more detail further down the page). | ||
====== Getting specific fasta sequences from reference file ====== | ====== Getting specific fasta sequences from reference file ====== | ||
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-outfmt 6 \ | -outfmt 6 \ | ||
-evalue 0.00001 | -evalue 0.00001 | ||
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+ | # the different columns in this output format are : | ||
+ | # Fields: query id, | ||
+ | subject id, | ||
+ | % identity, | ||
+ | alignment length, | ||
+ | mismatches, | ||
+ | gap opens, | ||
+ | query start, | ||
+ | query end, | ||
+ | subject start, | ||
+ | subject end, | ||
+ | evalue, | ||
+ | bit score | ||
</ | </ | ||
mkatari-bioinformatics-august-2013-blastnotes.txt · Last modified: 2015/06/04 12:38 by mkatari