amh: amh

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

Description

This function is for counting the number of "alternative / more proximal" microhomologies that were bypassed during repair the repair of a CRISPR deletion. It should be used on Sanger sequenced alleles already analysed by running mhq(input, CRISPResso=F). In the other scenario, When analysing CRISPResso output data, mhq automatically counts alternative microhomologies so this script is not necessary.

Usage

amh(input, genome)

Arguments

input	text file derived from output of mhq(yourData) with additional columns as specified below
genome	BSgenome object to pull sequences from. IMPORTANT: Has to be loaded before running the function. (i.e. genome <- BSgenome.Mmusculus.UCSC.mm9). Allows any BSgenome supported genome to be used.

Details

Input is a tab seperated text file (without column names) containing deletions in the same format as output by the mhq function but with some additional columns added. Bed file coordinates are best obtained using a tool like UCSC BLAT. Also requires the desired genome to be preloaded as a BSGenome object

• MutantSequence - same as mhq output

• ReferenceSequence - same as mhq output

• SizeOfDeletion - same as mhq output

• NumberOfReads - same as mhq output

• MH_amount - same as mhq output

• LD_chr - Additional: chromosome of deletion start

• LD_start - Additional: bed coordinate start of deletion span

• LD_stop - Additional: bed coordinate end of deletion span

• strand - Additional: strand that deletion was mapped to (or strand that microhomology is reported for)

• sg_start - Additional: bed coordinate start of sgRNAs span (if pairs of sgRNAs used, then start coordinate of 5' most sgRNA)

• sg_stop - Additional: bed coordinate end of sgRNAs span (if pairs of sgRNAs used, then end coordinate of 3' most sgRNA)

Output is the original dataframe but with two additional columns:

• altMH_count - Number of alternative microhomologies found

• add_delSize - Additional size of deletion beyond sgRNAs (same as deletion size when using one sgRNA)

Examples

genome <- BSgenome.Mmusculus.UCSC.mm9
amh(input="~/exampleData/Sanger/sequenceDataFile_altMH.txt", genome)

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