### The code is used in the linux system.
#Python environment and Cutadapt (version 2.10 or latest) needs to be installed before data processing. 

Installation on a Debian-based Linux distribution (https://cutadapt.readthedocs.io/en/stable/installation.html)

Cutadapt is also included in Debian-based Linux distributions, such as Ubuntu. Simply use your favorite package manager to install Cutadapt. On the command-line, this should work

sudo apt install cutadapt

or possibly

sudo apt install python3-cutadapt


############# The tso-mix index information. Index ID	Index sequence £¨5' of 1st read in pair-end£©
N4	^NNNNGGG
index1	^ATCACGNNNNGGG
index2	^CGATGTNNNNGGG
index3	^NNNNTTAGGCNGGG
########### The single cell barcodes information in barcode.txt. Barcodes (5' end of 2nd read in pair-end)
CGTGAT
ACATCG
GCCTAA
TGGTCA
CACTGT
ATTGGC
GATCTG
TCAAGT
CTGATC
AAGCTA
GTAGCC
TACAAG
TTGACT
GGAACT
TGACAT
GGACGG
CTCTAC
GCGGAC
TTTCAC
GGCCAC


################ If there are hunderds and more cells are in scm6A-seq data, tso-mix separation is needed.

sh ./scm6A-tsomix-separation.sh ${dir}/Test.fastq.gz

output file:
*index1.fastq
*index2.fastq
*index3.fastq
*N4.fastq

############## After tso-mix separation,cellular barcodes is needed for single cell reads isolation. Or if less than 20 cells in one library, single cell reads isolation is performed directlty. 
###In the "scm6A-seq reveals single-cell landscapes of the dynamic m6A during oocyte maturation and early embryonic development" manuscript, each library contains no more than 20 cells, so we only used this procedure.
### Test 10 thousand reads for single cell isolation with 6 cores, cost 1m24.507s

sh ./scm6A-SCbarcodes-isolation.sh

Expected output files:
*_${barcode}.fastq.gz