mhq: mhq

In d0minicO/mhscanR: Analysis of Microhomologies in CRISPR/Cas9 Deletions

Description

This function is for quantifying microhomologies in pre-mapped DNA sequencing of CRISPR/Cas9 deletions. It accepts targeted amplicon next-generation sequencing data already analysed using CRISPResso (1.0.x) (Pinello et al., 2016). Alternatively, it accepts any sequencing data (eg Sanger sequencing) that has already been processed using a local alignment tool (e.g. MUSCLE).

Usage

mhq(input, CRISPResso = TRUE)

Arguments

input	path to directory containing Allele_Frequency_tables.txt files or path to sequenceDataFile.txt
CRISPResso	Are you analysing CRISPResso Allele_frequency_table.txt files? (=TRUE/FALSE)

Details

When analysing CRISPResso data (CRISPResso=TRUE): Input directory should contain ONLY one or more Allele_frequency_table.txt files that were outputted by CRISPResso (1.0.x) (Pinello et al., 2016). No other .txt files should be in this directory. Output is a data frame (or list of data frames if multiple files are being analysed).

Also writes new .txt files to a new directory (/path/to/directory/MHQuant_out/MHQuant_out_Allele_Frequency_table.txt).

Output contains these tab seperated columns:

• MutantSequence - already determined by CRISPResso

• ReferenceSequence - already determined by CRISPResso

• SizeOfDeletion - already determined by CRISPResso

• NumberOfReads - already determined by CRISPResso

• MH_amount - microhomology amount found, if any, or 0

• MH_sequence - microhomology sequence found, if any, or "No_MH"

• altMH_count - alternative microhomologies found within the deleted sequence, if any, or "No_MH"

When analysing Sanger sequencing data (CRISPResso=FALSE): Input should be a single .txt file containing deletion alleles that were already aligned using a local alignment tool such as MUSCLE (Edgar, 2004). Input text file should contain five tab-seperated columns containing the DNA sequences of the breakpoints to be analysed. The length of each of the DNA sequences can be varied between rows, but must be the same between columns. See this example:

Example1 CGTGGCGAGG GCTGAGCTAT TGTTAGCACA GCTTCTCCA
Example2 CGTGGCGAGGCGTGG GCTGAGCTATGCTAT TGTTAGCACAGCACA GCTTCTCCACTCCA

• column1 - Sequence name

• column2 - 5' sequence not included in the deletion

• column3 - 5' sequence included in the deletion

• column4 - 3' sequence included in the deletion

• column5 - 3' sequence not included in the deletion

Examples

mhq(input="~/exampleData/CRISPResso/", CRSISPresso=TRUE)
mhq(input="~/exampleData/Sanger/sequenceDataFile.txt", CRSISPresso=FALSE)

d0minicO/mhscanR documentation built on May 4, 2021, 5:22 p.m.