# Getting L1_RS2 sequence from LINE1 consensus
[unalim@gra-login2 me_ref]$ awk '/>L1_RS2/,/ /' rm10_LINE_cons.fa

# Getting ERVK2 sequence from LTR consensus (in between fasta file)
[unalim@gra-login1 me_ref]$ sed -n '/>MacERVK2-int/,/>MacERVK2_LTR1a/{ />MacERVK2_LTR1a/!p }' rm10_LTR_cons.fa


# Building ZIP file
# Requirements: consensus sequence for transposon in ref genome (fa), repeat masked bed file

module load bowtie2 and samtools

# template
java -Xmx1G -jar ../melt/MELT.jar BuildTransposonZIP <fa> <bed> <name = ALU or LINE1> <error>
# for LINE1
java -Xmx1G -jar ../../melt/MELT.jar BuildTransposonZIP rm10_LINE_cons.fa rm10_L1.bed LINE1 3
# for Alu (AluY as a test)
java -Xmx1G -jar ../../melt/MELT.jar BuildTransposonZIP rm_AluY_cons.fa rm10_Alu.bed ALU 10
# note: command is also provided as executable batch file using salloc

# for error: ALU is 10 and LINE1 is 3

# forms ALU_MELT.zip and LINE1_MELT.zip
Archive:  ALU_MELT.zip
ALU.fa
ALU.fa.fai
ALU.bed
ALU.1.bt2
ALU.2.bt2
ALU.3.bt2
ALU.4.bt2
ALU.rev.1.bt2
ALU.rev.2.bt2
ALU.info