Question: Detecting Structural Variant From Chip Seq Data
1
gravatar for sara
6.1 years ago by
sara40
sara40 wrote:

Hi,

I am newbie to NGS data analysis.

I used BWA for aligning to reference genome and then samtool. Now am having bam file, sam file and VCF file. i used IGV browser to view the bam file in than i seen IGV uses color coding to flag anomalous insert sizes.

Red for an inferred insert size that is larger than expected (deletion) Blue for an inferred insert size that is smaller than expected (insertion)

i need to extract the deletion part from the bam file or samfile. can anybody give a suggestion of tools on how to extract this particular region ?

chipseq ngs • 2.0k views
ADD COMMENTlink modified 6.1 years ago by Sean Davis25k • written 6.1 years ago by sara40
1
gravatar for Sean Davis
6.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Some choices to try might include breakdancer (pe), delly (pe and sr), pindel (sr), and cnvnator (rd) where pe = paired-end, sr = split read, and rd = read depth. There are MANY other options and I would be reluctant to suggest which would be "best" for any given situation.

ADD COMMENTlink written 6.1 years ago by Sean Davis25k
1

Won't it be a problem to detect SV using chip-seq data? I though that chip-seq covers too short regions for SV calling.

ADD REPLYlink written 6.1 years ago by PoGibas4.8k
1

I agree that the false-negative rate may be very high, but for all but the read-depth approaches, there is at least the potential for these softwares to find something if it is present in the data. The original poster seems to believe that she can see a signal by eye.

ADD REPLYlink written 6.1 years ago by Sean Davis25k

@ Sean Davis, through visualization only i seen the signal. Since am new to this field i need help from expertise.

ADD REPLYlink written 6.1 years ago by sara40
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