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#!/bin/bash
#454 test examples
art_454=../art_454
#art_454=../../bin/MacOS64/art_454
#art_454=../../bin/Linux64/art_454
# 1) simulation of 454 single-end reads at 10X coverage using the built-in 454 FLX read profile
$art_454 -a -s ./testSeq.fa ./single_454_flx 10
# convert an aln file to a bed file
../aln2bed.pl single_454_flx.bed single_454_flx.aln
# 2) simulation of 454 paried-end reads at 5X coverage with the mean fragment size 500
# and standard deviation 20 using the built-in 454 FLX read profile
$art_454 -a -s ./testSeq.fa ./paired_454_flx 5 500 20
# convert both aln files to a bed file
../aln2bed.pl paired_454_flx.bed paired_454_flx1.aln paired_454_flx2.aln
# 3) simulation of 454 paried-end reads at 6X coverage with the mean fragment size 500
# and standard deviation 20 using the built-in 454 FLX Titanium read profile
$art_454 -a -s -t ./testSeq.fa ./paired_454_flxTitan 6 500 20
# convert both aln files to a bed file
../aln2bed.pl paired_454_flxTitan.bed paired_454_flxTitan1.aln paired_454_flxTitan2.aln
# 4) 5' end amplicon sequencing with 10 single-end reads per amplicon
$art_454 -a -s -A ./amplicon_reference.fa ./amp_single_454 10
# 5) both 5' and 3' ends amplicon sequencing with 5 read pairs per amplicon
$art_454 -a -s -B ./amplicon_reference.fa ./amp_paired_454 5
# 6) used a fixed random seed to generate identical datasets
$art_454 -a -s -r 777 ./testSeq.fa ./single_454_t1 10
$art_454 -a -s -r 777 ./testSeq.fa ./single_454_t2 10
# compare difference
echo "compare difference of two simulation datasets after normalising known difference"
sed 's?^\(@PG.*testSeq\.fa \./single_454_t\)2?\11?' single_454_t2.sam > single_454_t2_normalised.sam
diff single_454_t1.sam single_454_t2_normalised.sam
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