Daniel:Notebook/GenomeMiner/2013-7-22: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Djacobse
(Created page with "=HL155= Back to Calendar '''Converting Sam to Bam''' samtools view -bS hrcp_fullindex_samout.sam > hrcp_hl155.bam")
 
>Djacobse
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 3: Line 3:
[[Daniel:Notebook/GenomeMiner|Back to Calendar]]
[[Daniel:Notebook/GenomeMiner|Back to Calendar]]


'''Converting Sam to Bam'''
==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
'''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

Latest revision as of 22:14, 22 July 2013

HL155[edit]

Back to Calendar

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