Commit 7839f651 authored by Rebecca E Batorsky's avatar Rebecca E Batorsky
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added readme

parent 1b5651c1
# sdmmej
This is a repository to work on the error prone dna repair project with the McVey lab at Tufts University.
The script will be run like this on the command line, with a single argument that is the hifibr output file:
Rscript process_hifibr.R TestData_HiFiBR_Output_mod.csv
You need to have the tidyverse and Biostrings library installed.
It generates four output files in a directory like this:
Directory: TestData_HiFiBR_Output_mod_output
Files:
TestData_HiFiBR_Output_mod_reclassified.csv: same as input, but adds an “ID” column as well as a column for how the sequence was reclassified
TestData_HiFiBR_Output_mod_complex.txt: sequences that could not be reclassified as ins or del
TestData_HiFiBR_Output_mod_insertion.txt: all ins sequences
TestData_HiFiBR_Output_mod_deletion.txt: all del sequences with dashes
I added a few more sequences to the test data, the last three lines of the file TestData_HiFiBR_Output_mod.csv, which are:
1. Reference sequence
2. One sequence with <10 reads
3. One sequence with both SNP and deletion, which ends in the complex category because it can’t be reclassified
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