Daniel:Notebook/GenomeMiner/2013-7-26

From ZhangLabWiki
Revision as of 17:52, 26 July 2013 by >Djacobse
Jump to navigation Jump to search

HL155

Back to Calendar

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