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author plus91-technologies
date Thu, 19 Jun 2014 02:43:07 -0400
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1 SoftSearch: 1 SoftSearch:
2 2
3 --SoftSearch is a tools that uses soft-masked reads and discordant read pairs to identify structural variation(SV) in 3 --SoftSearch is a tool that uses soft-masked reads and discordant read pairs to identify structural variants(SV) in
4 illumina next-generation sequencing data. 4 Illumina paired-end next-generation sequencing data.
5 --It is a Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations. 5 --Using Soft Clipped reads in which one part of the read maps to the reference genome but the other part does not SoftSearch
6 --Breakpoint is a place or time at which an interruption or change is made. 6 can identify and call SVs including deletions, insertions, translocations, inversions, and tandem duplications
7 --SoftSearch requires only two inputs: a BAM file of aligned reads and fasta file of the genome to which the reads were aligned. 7 --SoftSearch requires two inputs: a BAM file of aligned reads and fasta file of the reference genome to which the reads
8 were aligned.
8 9
9 Google Code Link: 10 Google Code Link:
10 11
11 https://code.google.com/p/softsearch/ 12 https://code.google.com/p/softsearch/
12 13
14 Pre-Requirement: 15 Pre-Requirement:
15 16
16 -Perl 17 -Perl
17 -Bedtools 18 -Bedtools
18 -SamTools 19 -SamTools
19 Must have an entry in environment variable 20 Must be accessible from the PATH environment variable
20 21
21 ------------------------------------------------------------------------------------------------------------------ 22 ------------------------------------------------------------------------------------------------------------------
22 How To Selecte fasta file from Database (Additional Configuration): 23 How To Select fasta file from Database (Additional Configuration):
23 24
24 --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/ 25 --A fasta_indexes.loc file must be located in shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
25 8578d978014c/softsearch/tool-data/ 26 8578d978014c/softsearch/tool-data/
26 27
27 --open the fasta_indexes.loc file and make changes like 28 --open the fasta_indexes.loc file and add an entry according to the example below
28 29
29 <unique_build_id> <dbkey> <display_name> <file_base_path> 30 <unique_build_id> <dbkey> <display_name> <file_base_path>
30 31
31 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa 32 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
32 33
33 --open shed_tool_data_table_conf.xml file and add following. 34 --open shed_tool_data_table_conf.xml file and add the following
34 35
35 <tables> 36 <tables>
36 <table name="fasta_indexes" comment_char="#"> 37 <table name="fasta_indexes" comment_char="#">
37 <columns>value, dbkey, name, path</columns> 38 <columns>value, dbkey, name, path</columns>
38 <file path="/path/to/fasta_indexes.loc" /> 39 <file path="/path/to/fasta_indexes.loc" />