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comparison README @ 28:da3c9b9fb992 draft

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author plus91-technologies
date Thu, 19 Jun 2014 02:29:43 -0400
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1 SoftSearch:
2
3 --SoftSearch is a tools that uses soft-masked reads and discordant read pairs to identify structural variation(SV) in
4 illumina next-generation sequencing data.
5 --It is a Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations.
6 --Breakpoint is a place or time at which an interruption or change is made.
7 --SoftSearch requires only two inputs: a BAM file of aligned reads and fasta file of the genome to which the reads were aligned.
8
9 Google Code Link:
10
11 https://code.google.com/p/softsearch/
12
13 ------------------------------------------------------------------------------------------------------------------
14 Pre-Requirement:
15
16 -Perl
17 -Bedtools
18 -SamTools
19 Must have an entry in environment variable
20
21 ------------------------------------------------------------------------------------------------------------------
22 How To Selecte fasta file from Database (Additional Configuration):
23
24 --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
25 8578d978014c/softsearch/tool-data/
26
27 --open the fasta_indexes.loc file and make changes like
28
29 <unique_build_id> <dbkey> <display_name> <file_base_path>
30
31 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
32
33 --open shed_tool_data_table_conf.xml file and add following.
34
35 <tables>
36 <table name="fasta_indexes" comment_char="#">
37 <columns>value, dbkey, name, path</columns>
38 <file path="/path/to/fasta_indexes.loc" />
39 </table>
40 </tables>
41
42 ------------------------------------------------------------------------------------------------------------------
43 Authors:
44
45 ResearchDx
46 http://researchdx.com
47
48 Plus91 Technologies Private Limited
49 http://www.plus91.in/