Mercurial > repos > researchdx-plus91technologies > softsearch
comparison README @ 6:925f6330cd80 draft default tip
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author | researchdx-plus91technologies |
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date | Thu, 19 Jun 2014 08:43:52 -0400 |
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1 SoftSearch: | |
2 | |
3 --SoftSearch is a tool that uses soft-masked reads and discordant read pairs to identify structural variants(SV) in | |
4 Illumina paired-end next-generation sequencing data. | |
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 can identify and call SVs including deletions, insertions, translocations, inversions, and tandem duplications | |
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. | |
9 | |
10 Google Code Link: | |
11 | |
12 https://code.google.com/p/softsearch/ | |
13 | |
14 ------------------------------------------------------------------------------------------------------------------ | |
15 Pre-Requirement: | |
16 | |
17 -Perl | |
18 -Bedtools | |
19 -SamTools | |
20 Must be accessible from the PATH environment variable | |
21 | |
22 ------------------------------------------------------------------------------------------------------------------ | |
23 How To Select fasta file from Database (Additional Configuration): | |
24 | |
25 --A fasta_indexes.loc file must be located in shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/ | |
26 8578d978014c/softsearch/tool-data/ | |
27 | |
28 --open the fasta_indexes.loc file and add an entry according to the example below | |
29 | |
30 <unique_build_id> <dbkey> <display_name> <file_base_path> | |
31 | |
32 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa | |
33 | |
34 --open shed_tool_data_table_conf.xml file and add the following | |
35 | |
36 <tables> | |
37 <table name="fasta_indexes" comment_char="#"> | |
38 <columns>value, dbkey, name, path</columns> | |
39 <file path="/path/to/fasta_indexes.loc" /> | |
40 </table> | |
41 </tables> | |
42 | |
43 ------------------------------------------------------------------------------------------------------------------ | |
44 Authors: | |
45 | |
46 ResearchDx | |
47 http://researchdx.com | |
48 | |
49 Plus91 Technologies Private Limited | |
50 http://www.plus91.in/ |