Mercurial > repos > yating-l > hubarchivecreator_test
diff hub-archive-creator/test-data/tblastN/readme/README.md @ 6:9193fe3ee73f draft default tip
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| author | yating-l |
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| date | Thu, 22 Dec 2016 15:59:24 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hub-archive-creator/test-data/tblastN/readme/README.md Thu Dec 22 15:59:24 2016 -0500 @@ -0,0 +1,48 @@ +Conversion of NCBI BLAST+ tblastn results to PSL format +======================================================= +Wilson Leung <wleung@wustl.edu> + +Last Update: 04/24/2016 + + +Version information +------------------- +* Kent source tree: v324 +* NCBI BLAST+: BLAST 2.2.30+ + +Data sources +------------------- +For testing purposes, the database consists of only contig1 in the Dbia3 assembly while the protein sequences correspond to the three isoforms of the *D. melanogaster* *ci* gene in contig1. The protein sequences are available through [FlyBase](http://flybase.org/cgi-bin/getseq.html?source=dmel&id=FBgn0004859&chr=4&dump=PrecompiledFasta&targetset=translation). + +* Dbia3.fa = contig1 sequence in the Dbia3 asssembly +* ci.pep = Protein sequences for the three isoforms of the *ci* gene in *D. melanogaster* + +Conversion protocol +----------------------- +1. Create BLAST database for the assembly +``` +makeblastdb -in Dbia3.fa -dbtype nucl +``` + +2. Perform tblastn search and output results in XML format +``` +tblastn -outfmt 5 -db Dbia3.fa -query ci.pep -out tblastn_Dbia3_ci.xml -evalue 1e-2 +``` + +3. Convert results into PSL format +``` +blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl +``` + +4. Convert PSL output into BED format +``` +pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed +``` + +Output files +----------------------- +* tblastn_Dbia3_ci.xml = tblastn results in XML format +* tblastn_Dbia3_ci.xml.psl = tblastn results in PSL format +* tblastn_Dbia3_ci.xml.bed = tblastn results in BED format + +