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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