Mercurial > repos > plus91-technologies > softsearch
changeset 27:2006814aa6f3 draft
Deleted selected files
| author | plus91-technologies |
|---|---|
| date | Thu, 19 Jun 2014 01:42:45 -0400 |
| parents | 92d8479f1616 |
| children | da3c9b9fb992 |
| files | README |
| diffstat | 1 files changed, 0 insertions(+), 36 deletions(-) [+] |
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--- a/README Mon Jun 09 09:58:47 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -1.SoftSearch: - - --SoftSearch is a tools that uses soft-masked reads and discordant read pairs to identify structural variation(SV) in - illumina next-generation sequencing data. - - --It is a Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations. - - --Breakpoint is a place or time at which an interruption or change is made. - - --SoftSearch requires only two inputs: a BAM file of aligned reads and fasta file of the genome to which the reads were aligned. - - -2.Setting for selecting fasta file from database. - - --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/ - 8578d978014c/softsearch/tool-data/ - - --open the fasta_indexes.loc file and make changes like - - <unique_build_id> <dbkey> <display_name> <file_base_path> - - eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa - - --open shed_tool_data_table_conf.xml file and add following. - - <tables> - <table name="fasta_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="/path/to/fasta_indexes.loc" /> - </table> - </tables> - - -Notes: - --Need latest version of Samtools(version above 0.1.18) and perl installed on local system. -