Daniel:Notebook/GenomeMiner/2013-8-12
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HL155
From the talk I had with Matt last week, I have changed my strategy. Now I'll be following his pipeline, since it seems to be more rigorous analysis than mine.
My commands
Sam > Bam and sort Bam
samtools view -bS hrcp_fullindex_samout.sam | samtools sort - hrcp_sorted_hl155 &
Filter and convert back to sam
samtools view -h -F 4 -q 8 hrcp_sorted_hl155.bam > hrcp_sorted_filtered_hl155.sam &
Convert back to sam
samtools view -bS hrcp_sorted_filtered_hl155.sam > hrcp_sorted_filtered_hl155.bam &
Replace matched reads with equals
samtools calmd -eS hrcp_sorted_filtered_hl155.sam probeseq/Probelist_all.fa > hrcp_sortfilt_eq.sam &