checkPrimer: checkPrimer

In robinweide/tagmeppr: A computational pipeline to map tagmap-insertions

Description

This tool checks the assumptions about the primers.

Usage

checkPrimer(fwdPrimer, revPrimer, exp, ITR = "PiggyBac")

Arguments

fwdPrimer	A character-string of the forward-primer used.
revPrimer	A character-string of the reverse-primer used.
exp	The tagMeppr-object of a sample: first run align.
ITR	Can take PiggyBac (default), SleepingBeauty, or a path to a 1000xN-padded ITR.fasta.

Details

The expected general layout for the ITR-sequence looks like this:

|---ITR---NNN...NNN---ITR---|

The primers are expected to be 5'-end for the reverse and 3' for the forward:

<rev |---ITR---NNN...NNN---ITR---| fwd>

This tool checks these assumptions and sets the rev5_fwd3 flag to TRUE.

Value

The experiment-object will be updated with the rev5_fwd3-flag, which will tell all downstream analyses if our assumptions are correct.

Author(s)

Robin H. van der Weide, [e-mail]

Examples

## Not run: 

C9 = newTagMeppr(F1 = 'clone9_FWD_R1.fq.gz',
                 F2 = 'clone9_FWD_R2.fq.gz',
                 R1 = 'clone9_REV_R1.fq.gz',
                 R2 = 'clone9_REV_R2.fq.gz',
                 name = "clone9",
                 protocol = 'PiggyBac')

checkPrimer(fwdPrimer = "CGTCAATTTTACGCAGACTATC",
            revPrimer = "GTACGTCACAATATGATTATCTTTCTAG",
            exp =  C9,
            ITR = 'PiggyBac')


## End(Not run)

robinweide/tagmeppr documentation built on Feb. 26, 2020, 10:41 p.m.