Question: Finding difference in read depth between two BAM files
0
gravatar for gtasource
2.3 years ago by
gtasource30
gtasource30 wrote:

Hello,

I am looking to find the difference in read depth between two bam files (A, B.) My initial idea was to use Bedtools, find the total coverage of A and B, and then use Bedtools intersect to compare where they overlap and do not. However, I'm just curious if anybody has alternative suggestions or better software tools to use.

sequencing bam bedtools • 880 views
ADD COMMENTlink modified 2.3 years ago by Pierre Lindenbaum127k • written 2.3 years ago by gtasource30

What data it is ? ChIP ? WGS ? RNA ?

ADD REPLYlink written 2.3 years ago by geek_y10k
2
gravatar for Pierre Lindenbaum
2.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

using samtools mpileup and two bam files:

samtools mpileup -f ref.fasta in1.bam in2.bam | cut -f 1,2,4,7

1   101766  19  29
1   101767  19  30
1   101768  19  29
1   101769  123 188
1   101770  122 187
1   101771  122 189
1   101772  122 189

output is : chrom/pos/depth-bam1/depth-bam2

ADD COMMENTlink written 2.3 years ago by Pierre Lindenbaum127k

update:

samtools depth in1.bam in2.bam
ADD REPLYlink written 8 months ago by Pierre Lindenbaum127k
0
gravatar for Hussain Ather
2.3 years ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

There are a few methods....

  • genomeCoverageBedtools
  • samtools depth
  • deeptools bamcoverage
  • Rsamtools
ADD COMMENTlink written 2.3 years ago by Hussain Ather940
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