Mercurial > repos > plus91-technologies > softsearch
comparison README @ 26:92d8479f1616 draft
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| author | plus91-technologies |
|---|---|
| date | Mon, 09 Jun 2014 09:58:47 -0400 |
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| 25:06e32c8b5682 | 26:92d8479f1616 |
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| 1 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 | |
| 6 --It is a Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations. | |
| 7 | |
| 8 --Breakpoint is a place or time at which an interruption or change is made. | |
| 9 | |
| 10 --SoftSearch requires only two inputs: a BAM file of aligned reads and fasta file of the genome to which the reads were aligned. | |
| 11 | |
| 12 | |
| 13 2.Setting for selecting fasta file from database. | |
| 14 | |
| 15 --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/ | |
| 16 8578d978014c/softsearch/tool-data/ | |
| 17 | |
| 18 --open the fasta_indexes.loc file and make changes like | |
| 19 | |
| 20 <unique_build_id> <dbkey> <display_name> <file_base_path> | |
| 21 | |
| 22 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa | |
| 23 | |
| 24 --open shed_tool_data_table_conf.xml file and add following. | |
| 25 | |
| 26 <tables> | |
| 27 <table name="fasta_indexes" comment_char="#"> | |
| 28 <columns>value, dbkey, name, path</columns> | |
| 29 <file path="/path/to/fasta_indexes.loc" /> | |
| 30 </table> | |
| 31 </tables> | |
| 32 | |
| 33 | |
| 34 Notes: | |
| 35 --Need latest version of Samtools(version above 0.1.18) and perl installed on local system. | |
| 36 |