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 Sam to Bam'''
'''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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  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

Revision as of 20:52, 22 July 2013

HL155

Back to Calendar

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