Pipeline code for Sequential-GAM(Genome Architecture Mapping).

mapping include the whole processing of mapping.

usage: bash Cell_name

1.removing the adaptor by trim_galore

parameters are:

trim_galore -q 20 --stringency 3 --length 20 --nextera -o ${dir_out} -e 0.1 --gzip --paired ${dir_in}"Cleandata/"${fast1} ${dir_in}"Cleandata/"${fast2}

2.mapping reads by bowtie2

parameters are:

bowtie2 -p 10 -5 15 -x /home/ygli/index/CAST -1 B2F_NP1_R1.fq.gz -2 B2F_NP1_R2.fq.gz -S B2F_NP1_C.sam

3.removing duplicates with samtools and Picard Toolkit

parameters are:

samtools view -f 0x2 -bSB10F-NP252_S.sam > B10F-NP252_S.bam

samtools sort B10F-NP252_S.bam > B10F-NP252_S.sort.bam

samtools index B10F-NP252_S.sort.bam

java -jar /home/ygli/tools/picard.jar MarkDuplicates REMOVE_DUPLICATES=True I=B10F-NP252_C.sort.bam O=B10F-NP252_C.sort.remove_dump.bam M=B10F-NP252_C.sort.marked_dup_metrics.txt

capture table

1.calculating the capture or not for each window with given resolution (10kb in codes)


2.merge capture situation in each cell into one table



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