Question: GC-BIAS correction for BAM file
2
gravatar for amitgsir
3.0 years ago by
amitgsir50
Incheon, South Korea
amitgsir50 wrote:

Hi,

I am looking for any software which can correct the GC-Bias in the BAM file and provides the output as BAM.

I know that deeptools (correctGCBias) does the exactly same job, but the output of the deeptools is variable in each run.

So, I am looking for more specific tool.

Basically, I want to count the sequence reads for each chromosome in NIPT (low depth, WGS sample) BAM file after the GC-Bias correction.

Many LOESS based or R-based GC-bias correction methods are available, but they provides the output as normalized data, not as total number of reads in each chromosome/ specified region.

Any suggestions?

deeptools rna-seq R genome • 1.8k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 3.0 years ago by amitgsir50
2
gravatar for Devon Ryan
3.0 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

The reason correctGCBias can produce slightly different results each time is due to using a random number at one point. If you really need to produce the exact same results each time then you could hardcode a seed in. I expect that adding the following near the top of deeptools/correctGCBias.py will do that:

np.random.seed(1234)
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Devon Ryan88k
2

Yeah,

Fixing the seed using np.random.seed(1234) is giving the exact same results each time.

Thanks

ADD REPLYlink written 3.0 years ago by amitgsir50
1

Great, glad that worked!

ADD REPLYlink written 3.0 years ago by Devon Ryan88k
1

Thanks Ryan, I will try this and will inform you if this works.

ADD REPLYlink written 3.0 years ago by amitgsir50
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