Commit 948ed84b authored by Rebecca E Batorsky's avatar Rebecca E Batorsky
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This is a repository to work on the error prone dna repair project with the McVey lab at Tufts University.
**Dependencies***
**Dependencies**
Python 2.7
Python libraries: pandas
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R libraries: tidyverse, Biostrings
**Pipeline Script**
This script takes one input: the path to the HiFibr output file
This script takes the path to the HiFibr output file as the single command line argument.
Other default arguments are set within the script.
Example usage on test data:
`sh run_pipeline.sh test_data/polyA1Seq/PolyA1Seq_testdata.csv`
It generates four output files in a directory `PolyA1Seq_testdata_output`
It generates output files in a directory `PolyA1Seq_testdata_output`
Files:
- Outputs from Hifibr processing script
`PolyA1Seq_testdata_reclassified.csv` Same format input, but adds an “ID” column as well as a column for how the sequence was reclassified
`PolyA1Seq_testdata_complex.txt` sequences that could not be reclassified as ins or del
`PolyA1Seq_testdata_insertion.txt` all ins sequences
`PolyA1Seq_testdata_deletion.txt` all del sequences with dashes
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`PolyA1Seq_testdata_deletion.txt` all del sequences with dashes
- Outputs from Deletion script
`PolyA1Seq_testdata_deletion_consistency_log.txt`
`PolyA1Seq_testdata_deletion_consistency_table.txt`
- Outputs from Insertoin script
`PolyA1Seq_testdatatestdata_insertion_consistency2.csv`
`PolyA1Seq_testdatatestdata_insertion_consistency_long2.csv`
`PolyA1Seq_testdatatestdata_insertion_alignment2.csv`
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