Mercurial > repos > yating-l > hubarchivecreator

annotate test-data/tblastN/readme/README.md @ 0:f493979f1408 draft default tip

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