Question: How can you check if the downsampler in indeed random and efficient
0
gravatar for shruti
3.8 years ago by
shruti0
shruti0 wrote:

Hi, I am using the Picard downsampler for downsampling around 50 million reads from the entire human transciptome for my experiment. I want to know if the downsampler is indeed random and not creating bias. Is there anyway I can check that ? 

-Shruti

rna-seq • 945 views
ADD COMMENTlink written 3.8 years ago by shruti0

Downsampling reads from a bam file using DownsampleSam?

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by geek_y10k

Yes, i've used tophat for generating the BAM files from which I have used DownsampleSam from Picard.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by shruti0
1
gravatar for geek_y
3.8 years ago by
geek_y10k
Barcelona
geek_y10k wrote:

One way is to validate the results by generating different random sets and compare them wrt your goal. For e.g. If you have annotations, you can do quantification of genes, and check if they correlate between different random sets to get an idea.

Otherwise, if you go into details, it uses java.util.Random, which depends on ["Linear congruential generator"] algorithm to generate random numbers.

ADD COMMENTlink modified 14 months ago by RamRS25k • written 3.8 years ago by geek_y10k

Thank you @Goutham ! 

ADD REPLYlink written 3.8 years ago by shruti0
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