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26
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1 1.SoftSearch:
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2
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3 --SoftSearch is a tools that uses soft-masked reads and discordant read pairs to identify structural variation(SV) in
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4 illumina next-generation sequencing data.
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5
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6 --It is a Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations.
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7
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8 --Breakpoint is a place or time at which an interruption or change is made.
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9
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10 --SoftSearch requires only two inputs: a BAM file of aligned reads and fasta file of the genome to which the reads were aligned.
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11
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12
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13 2.Setting for selecting fasta file from database.
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14
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15 --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
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16 8578d978014c/softsearch/tool-data/
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17
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18 --open the fasta_indexes.loc file and make changes like
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19
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20 <unique_build_id> <dbkey> <display_name> <file_base_path>
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21
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22 eg: hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
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23
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24 --open shed_tool_data_table_conf.xml file and add following.
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25
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26 <tables>
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27 <table name="fasta_indexes" comment_char="#">
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28 <columns>value, dbkey, name, path</columns>
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29 <file path="/path/to/fasta_indexes.loc" />
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30 </table>
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31 </tables>
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32
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33
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34 Notes:
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35 --Need latest version of Samtools(version above 0.1.18) and perl installed on local system.
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36
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