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Changing to our iRODS directory

icd /iplant/home/shared/ucd.tomato/ti-2013

Preparing FASTQ sequence files

Quality filter FASTQ file

fastq_quality_filter -v -Q33 -q 20 -p 90 -i ID.fq -o q20p90.ID.fq

FASTQC quality analysis

fastqc

index FASTA file (only needs to be done once)

bwa index ITAG2.3_cdna_SHORTNAMES.fasta

align FASTQ file to reference

bwa aln -f q20p90.ID.sai -t 2 ITAG2.3_cdna_SHORTNAMES.fasta q20p90.ID.fq

convert sequence alignment index (.sai) file to .sam format

bwa samse -n1 -f q20p90.ID.sam ITAG2.3_cdna_SHORTNAMES.fasta q20p90.ID.sai q20p90.ID.fq

convert .sam file to binary .bam format

samtools view -Sb q20p90.ID.sam > q20p90.ID.bam

indexing .bam file

samtools index q20p90.ID.sort.bam