bsrate 3.0.1 and 3.3.1 have difference of BS conservation rate

[Ian Chang]

Hi, 

About one year ago, I used rmapbs-pe (download date: Aug 6, 2013) to map BS-Seq reads against mm9 genome. Then I used methpipe 3.0.1 to analyze the mapping results.

Recently, we got new BS-Seq data and then I used the same rmapbs-pe program and new methpipe 3.3.1 to process the data.

I found bsrate 3.0.1 have ~3% higher conversion rate than that of bsrate 3.3.1 (from ~98% to ~95%).

I have three questions:

1. Should I use the latest rmapbs-pe to remap the BS-Seq data?
2. What cause the difference between bsrate 3.0.1 and 3.3.1, which one should I use?
3. Do you have any suggestion to filter reads with low conversion rates?

I attached two bsrate results in this post.

Thanks.

Ian

[Meng Zhou]

Hi Ian,

I don't quite understand your case. Did you mean that you processed new data with latest version of methpipe? If you are comparing different data sets, it's normal that they have different BS conversion rate.

Best regards,
Meng

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[Ian Chang]

Hi Meng,

I used 3.0.1 and 3.3.1 to analyze both old and new data in the following steps

1. rmapbs-pe (Aug, 6, 2013)

2. duplicate-remover (3.3.1)

3. bsrate (3.0.1 vs 3.3.1)

The difference between bsrate 3.0.1 and 3.3.1 can be found in all data sets

Ian

[Andrew Smith]

Can you respond with a tiny sample of reads after removing duplicates? Maybe 100k of them? That would help us in debugging this.