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 [2015/06/04 12:38] (current) – mkatari | ||
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[[mkatari-bioinformatics-august-2013|Back to Manny' | [[mkatari-bioinformatics-august-2013|Back to Manny' | ||
+ | |||
+ | 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. | ||
+ | |||
+ | **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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< | < | ||
module load blast | module load blast | ||
- | which blastx | + | which blastn |
- | / | + | / |
</ | </ | ||
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#SBATCH -n 8 | #SBATCH -n 8 | ||
- | / | + | module load blast |
+ | |||
+ | echo "Blast ready to run" | ||
+ | |||
+ | blastn | ||
+ | -out scaffold12498.cassavaV5_2.bout \ | ||
+ | --num_threads 8 -outfmt 6 -evalue 0.00001 | ||
+ | |||
+ | echo "Blast complete" | ||
</ | </ | ||
+ | |||
* Run the sbatch file. As soon as you run the file a job id will be assigned to your submission. | * Run the sbatch file. As soon as you run the file a job id will be assigned to your submission. | ||
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-out $OUTPUT | -out $OUTPUT | ||
-num_threads 8 \ | -num_threads 8 \ | ||
- | -outfmt 6 | + | -outfmt 6 \ |
-evalue 0.00001 | -evalue 0.00001 | ||
+ | |||
+ | # 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.1405068790.txt.gz · Last modified: 2014/07/11 08:53 by mkatari