Daniel:Notebook/GenomeMiner/2013-7-26
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HL155[edit]
Yesterday's SAM to BAM didn't work, so I did it again.
Converting SAM to BAM
samtools view -bS hrcp_fullindex_samout.sam > hrcp_hl155.bam
Sorting BAM file
samtools sort hrcp_hl155.bam hrcp_sorted_hl155
Create BAM index file
samtools index hrcp_sorted_hl155.bam hrcp_sorted_hl155.bai
Create SAMfile of only mapped reads
samtools view -h -F 4 hrcp_sorted_hl155.bam > hrcp_onlymapped_hl155.sam
This last file ("hrcp_onlymapped_hl155.sam") should only contain mapped reads and is 1/4 the size of the original samfile, which should make it considerably easier to loop through.