Daniel:Notebook/GenomeMiner/2013-7-22: Difference between revisions
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[[Daniel:Notebook/GenomeMiner|Back to Calendar]] | [[Daniel:Notebook/GenomeMiner|Back to Calendar]] | ||
'''1. Converting | ==SAMtools== | ||
'''1. Converting SAM to BAM''' | |||
samtools view -bS hrcp_fullindex_samout.sam > hrcp_hl155.bam | samtools view -bS hrcp_fullindex_samout.sam > hrcp_hl155.bam | ||
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''Alternate Pipeline'' (Can be used instead of 1 and 2) | ''Alternate Pipeline'' (Can be used instead of 1 and 2) | ||
samtools view -bS hrcp_fullindex_samout.sam | samtools sort - hrcp_sorted_hl155 | samtools view -bS hrcp_fullindex_samout.sam | samtools sort - hrcp_sorted_hl155 | ||
'''3. Create BAM index file''' | |||
samtools index hrcp_sorted_hl155.bam hrcp_sorted_hl155.bai | |||
'''4. View Mapped Reads Only''' | |||
samtools view -h -F 4 hrcp_sorted_hl155.bam > hrcp_mapped_hl155.bam |
Latest revision as of 22:14, 22 July 2013
HL155[edit]
SAMtools[edit]
1. Converting SAM to BAM
samtools view -bS hrcp_fullindex_samout.sam > hrcp_hl155.bam
2. Sorting BAM file
samtools sort hrcp_hl155.bam hrcp_sorted_hl155
Alternate Pipeline (Can be used instead of 1 and 2)
samtools view -bS hrcp_fullindex_samout.sam | samtools sort - hrcp_sorted_hl155
3. Create BAM index file
samtools index hrcp_sorted_hl155.bam hrcp_sorted_hl155.bai
4. View Mapped Reads Only
samtools view -h -F 4 hrcp_sorted_hl155.bam > hrcp_mapped_hl155.bam