Daniel:Notebook/GenomeMiner/2013-8-12: Difference between revisions
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'''Sam > Bam and sort Bam''' | '''Sam > Bam and sort Bam''' | ||
samtools view -bS hrcp_fullindex_samout.sam | samtools sort - hrcp_sorted_hl155 & | 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 & |
Revision as of 18:35, 12 August 2013
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 &