GitHub - nicolaprezza/test-bs-aligner: shell scripts to generate a BS experiment dataset and test on it a BS aligner + methylation caller

The main script of this pipeline is pipeline_bismark_and_erne.sh. The pipeline simulates a methylation experiment, executes the erne/bismark aligners and methylation callers, and counts the number of correctly called methylations and total number of called methylations. To modify parameters of the simulation, edit testcase-bs-aligner-default.sh.

Name		Name	Last commit message	Last commit date
Latest commit History 8 Commits
README.md		README.md
README.md~		README.md~
README~		README~
compare_meth_annotations.sh		compare_meth_annotations.sh
compare_meth_annotations.sh~		compare_meth_annotations.sh~
compare_meth_annotations_cov_format.sh		compare_meth_annotations_cov_format.sh
compare_meth_annotations_cov_format.sh~		compare_meth_annotations_cov_format.sh~
compare_meth_annotations_cytosine_format.sh		compare_meth_annotations_cytosine_format.sh
compare_meth_annotations_cytosine_format.sh~		compare_meth_annotations_cytosine_format.sh~
compare_meth_annotations_erne_format.sh		compare_meth_annotations_erne_format.sh
pipeline_bismark_and_erne.sh		pipeline_bismark_and_erne.sh
pipeline_bismark_and_erne.sh~		pipeline_bismark_and_erne.sh~
pipeline_bismark_and_erne_small.sh		pipeline_bismark_and_erne_small.sh
pipeline_bismark_and_erne_small.sh~		pipeline_bismark_and_erne_small.sh~
pipeline_erne.sh		pipeline_erne.sh
pipeline_erne.sh~		pipeline_erne.sh~
sam-paired-to-fastq.sh		sam-paired-to-fastq.sh
testcase-bs-aligner-default.sh		testcase-bs-aligner-default.sh
testcase-bs-aligner-default.sh~		testcase-bs-aligner-default.sh~
testcase-bs-aligner.sh		testcase-bs-aligner.sh

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