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comparison test-data/tblastN/readme/README.md @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
| author | yating-l |
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| date | Wed, 21 Dec 2016 12:13:04 -0500 |
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| -1:000000000000 | 0:f493979f1408 |
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| 1 Conversion of NCBI BLAST+ tblastn results to PSL format | |
| 2 ======================================================= | |
| 3 Wilson Leung <wleung@wustl.edu> | |
| 4 | |
| 5 Last Update: 04/24/2016 | |
| 6 | |
| 7 | |
| 8 Version information | |
| 9 ------------------- | |
| 10 * Kent source tree: v324 | |
| 11 * NCBI BLAST+: BLAST 2.2.30+ | |
| 12 | |
| 13 Data sources | |
| 14 ------------------- | |
| 15 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). | |
| 16 | |
| 17 * Dbia3.fa = contig1 sequence in the Dbia3 asssembly | |
| 18 * ci.pep = Protein sequences for the three isoforms of the *ci* gene in *D. melanogaster* | |
| 19 | |
| 20 Conversion protocol | |
| 21 ----------------------- | |
| 22 1. Create BLAST database for the assembly | |
| 23 ``` | |
| 24 makeblastdb -in Dbia3.fa -dbtype nucl | |
| 25 ``` | |
| 26 | |
| 27 2. Perform tblastn search and output results in XML format | |
| 28 ``` | |
| 29 tblastn -outfmt 5 -db Dbia3.fa -query ci.pep -out tblastn_Dbia3_ci.xml -evalue 1e-2 | |
| 30 ``` | |
| 31 | |
| 32 3. Convert results into PSL format | |
| 33 ``` | |
| 34 blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl | |
| 35 ``` | |
| 36 | |
| 37 4. Convert PSL output into BED format | |
| 38 ``` | |
| 39 pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed | |
| 40 ``` | |
| 41 | |
| 42 Output files | |
| 43 ----------------------- | |
| 44 * tblastn_Dbia3_ci.xml = tblastn results in XML format | |
| 45 * tblastn_Dbia3_ci.xml.psl = tblastn results in PSL format | |
| 46 * tblastn_Dbia3_ci.xml.bed = tblastn results in BED format | |
| 47 | |
| 48 |