PE100 and PE150

[yuchenjulia]

Awesome work! But I am still confused about how to generate PE100 and PE150 annotation for hg38. Do you have some information? In the current package, only SR50 annotations are provided.

Thanks a lot!
Julia

[aliahhawari]

I'm interested to know about this too. Are there any follow ups?

[kandabarau]

would be great to hear anything on that topic.

even having a recipe for SE50 I do not know how to generalize to PE150. 1000genomes fastqs are PE100 so is this ok to use those? Or should we crop our reads to PE100 and use with bins annotated for 1kgenomes PE100 ?

thank you in advance!

[asntech]

Hi @kandabarau, we've using these annotations for sWGS data with PE150. You don't need to trim reads in your data.
For sure, benchmarking will be ideal to find any differences.

[kandabarau]

Hi @kandabarau, we've using these annotations for sWGS data with PE150. You don't need to trim reads in your data. For sure, benchmarking will be ideal to find any differences.

Dear Aziz @asntech ,
thank you for your reply. do you mean you are using your QDNAseq.hg38 default SE50 as background for PE150 data?
Or you are using 1000g PE100 as controls for PE150 data without trimming of the latest?

Thank you!

fyi @Overnightology