Daniel:Notebook/GenomeMiner/2013-8-12: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Djacobse
No edit summary
>Djacobse
No edit summary
Line 9: Line 9:
'''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

Back to Calendar

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 &