View Extract Reads from Assemblies
Mapping the reads to assembly
/data/process/Roya/assemblies/illuminaAssembly/CLCAssembly$ clc_ref_assemble_long -o Hv387CLCTag.fasta.cas -d Hv387CLCTag.fasta -q -p fb ss 100 400 ../Hv387_trim_NoDuplicatesTag.fasta
Convert casfile to bam
/opt/CLC/clc-assembly-cell-4.0.1beta-linux_64/castosam -a Hv387CLCTag.fasta.cas -o Hv387CLCTag.fasta.cas.bam
Sort bam file
samtools sort Hv387CLCTag.fasta.cas.bam Hv387CLCTag.fasta.cas.bam.sorted
samtools index Hv387CLCTag.fasta.cas.bam.sorted.bam
samtools view -h -f 0×0040 Hv387CLCTag.fasta.cas.bam.sorted.bam > tmp.sam