Commit ba3454d1 authored by Rebecca E Batorsky's avatar Rebecca E Batorsky
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edit readme

parent 948ed84b
......@@ -5,9 +5,11 @@ This is a repository to work on the error prone dna repair project with the McVe
**Dependencies**
Python 2.7
Python libraries: pandas
R >=3.5
R libraries: tidyverse, Biostrings
**Pipeline Script**
......@@ -22,16 +24,19 @@ Example usage on test data:
It generates output files in a directory `PolyA1Seq_testdata_output`
- 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
- 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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