Daniel:Notebook/GenomeMiner/2013-8-12: Difference between revisions
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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 | '''Convert back to bam''' | ||
samtools view -bS hrcp_sorted_filtered_hl155.sam > hrcp_sorted_filtered_hl155.bam & | samtools view -bS hrcp_sorted_filtered_hl155.sam > hrcp_sorted_filtered_hl155.bam & | ||
'''Replace matched reads with equals''' | '''Replace matched reads with equals''' | ||
samtools calmd -eS hrcp_sorted_filtered_hl155.sam probeseq/Probelist_all.fa > hrcp_sortfilt_eq.sam & | 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]
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.