Mapping illumina seq data Part 1
Mapping illumina seq data Part 1
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Utilizes BWA for mapping of illumina sequencing data. Default settings (customizable) for a species to be mapped to a divergent genome reference and to output a BAM file. Used with; SNP calling illumina seq data Part2 to output SNP calls.
Quick Start
- To use Mapping illumina seq data Part 1, import your data in FASTQ format.
- Resources: http://bio-bwa.sourceforge.net and http://samtools.sourceforge.net/samtools.shtml
Test Data
Test data for this app appears at the following links
Wild type parental data: http://de.iplantcollaborative.org/dl/d/D14B9BF1-EF7C-4395-8D4B-B86193B222A6/Parent_RIL71_pseudo_50bp.fastq
Mutant parental data: http://de.iplantcollaborative.org/dl/d/0F019C67-48AA-41FA-B01C-4D972C8472CB/Parent_RIL25_pseudo_50bp.fastq
Bulk segregant mutant sample data: http://de.iplantcollaborative.org/dl/d/6B6B53E5-B545-4FBD-9535-DC3DF1928905/BulkB_TGACCA_50bp.fastq
Input File(s)
Use one of the files above as test input. Our pseudo wheat genome reference sequence to complement the test datasets (as detailed Gardiner et al., 2014: doi: 10.1111/tpj.12660) can be found at: http://de.iplantcollaborative.org/dl/d/12BD9EC9-EABF-4B9C-9B31-7143F6FCB126/Wheat_new_array_AH_sequence.fas
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Default parameters only, no further configuration needed.
Output File(s)
Expect a sorted BAM file as output. For the first test case, the output file you will find at the link: http://de.iplantcollaborative.org/dl/d/58DA9AAF-597F-4BE3-B9F4-ECFA19B583F4/bwa_output.sorted.21668.bam