mmtv插入位点的分析

##从R1里取出含有引物的reads##

grep AAGGTTCTGATCTGAGCTCTGAGTGTTCTATTTTCCTATGTTCTTTTGGAATCTATCCAAGTCTTA LTR3-2_L4_P704504.R1.clean.fastq -B 1 > 704504-R1.txt

##提取R1 reads的header##

awk 'BEGIN {OFS = "\n"} {header = $0 ; getline seq ; getline qheader ; if (length(seq) >= 2 && length(seq) <= 251) {print header}}' 704504-R1.txt > 704504-R1-id.txt

##将R1 reads header转换成R2中对应的header##

awk '{print $1,"2:N:0:GAGATTCC+GGCTCTGA"}' 704504-R1-id.txt > 704504-R1-ID.txt

##提取出R2的reads##

grep -F -f 704504-R1-ID.txt LTR3-2_L4_P704504.R2.clean.fastq -A 1 > 704504-R2-reads.txt