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

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'''Filter and convert back to sam'''
'''Filter and convert back to sam'''
samtools view -h -F 4 -q 8 hrcp_sorted_hl155.bam > hrcp_sorted_filtered_hl155.sam &


samtools view -h -F 4 -q 8 hrcp_sorted_hl155.bam > hrcp_sorted_filtered_hl155.sam &
'''Convert back to bam'''
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 &
 
Matt's perl script isn't quite formatted for the way I formatted my reference .fa file, so I'm going to have to look over what to change.

Latest revision as of 20:17, 27 August 2013

HL155[edit]

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[edit]

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 bam

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 &

Matt's perl script isn't quite formatted for the way I formatted my reference .fa file, so I'm going to have to look over what to change.