scATAC-seq index designer

Time-stamp: "2017-11-01 14:57:52"

Two round barcoding multiplex

From An Introduction to Next-Generation Sequencing Technology by Illumina.

Requirements for a barcodes design

• -d: Hamming distance between every two barcodes >=4(of 8bp): for possible sequencing error
• -gmax and gmin: GC content 37.5-62.5% : for sequencer
• -n: max number of repeat bps [3]

Algorithm

Usage

$chmod u+x scATAC_index_designer
$scATAC_index_designer -h

 Usage: scATAC_index_designer [-h] [-l LEN] [-d DIST] [-o FNAME] [-gmax GC_MAX] [-gmin GC_MIN] [-n NUM_REPEAT] [-s SED]
 
 Barcode Design for scATAC.
 
 Options:
   -h, --help            show this help message and exit
   -l LEN                barcode length [8].
   -d DIST               min pair-wise distance between two generated barcodes.
   -a GC_MAX, --gmax=GC_MAX
                         max gc content.
   -i GC_MIN, --gmin=GC_MIN
                         min gc content.
   -n NUM_REPEAT         max repeat letters allowed.
   -s SED                sed barcodes to start with.
   -o FNAME              output file.

$scATAC_index_designer -l 8 -d 4 -o i7.4mm.txt --gmax 0.625 --gmin 0.375  -n 3
scATAC_index_designer -l 8 -d 4 -o ./examples/idx.4mm.txt --gmax 0.625 --gmin 0.375  -n 3  -s ./examples/old.txt