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Using the Hsf1 ChIPseq data from de Jong et al 2017, we can test StrainID's ability to identify the BY4742 strain background. This commit includes the metadata and README updates including placeholders for results and log directories. SraRunInfo.csv pulled from NCBI SRA search.
This commit includes the PBS script for downloading the FASTQ files from the Sra metadata associated with de Jonge 2017. The `.gitignore` file is updated appropriately to ignore log and FASTQ files.
This commit includes scripts and setup needed to align the BY4742 ChIPseq data which includes some ABI SOLiD data. `paper/setup.sh` was updated to create a bowtie colorspace index of sacCer3 for the ABI samples `paper/.gitignore` was updated to include the BAM alignment output `paper/BY4742-chipseq/job01_align_data.pbs` is the PBS script to call either BWA or bowtie (as appropriate for sequencing platform used) to align the raw FASTQ data.
This PBS script wraps up a sample-by-sample run of calling StrainID on all the BY4742 samples.
The .gitignore file is updated with the output from StrainID running on BY4742 data
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This pull request includes all the commits related to processing some BY4742 ChIPseq and MNase data and running StrainID on them to determine how well StrainID performs on distinguishing BY4742 from BY4741 and other strains