Chip-seq balcklisted region information for the latest version of genome ensembl GRCm38

Question

[luckysardar171]

Hello

Chip-data which I have mapped with the recent Mus_musculus.v103 from ensembl, I wanted blacklisted region for this genome because of coordinate may vary in different genome version can not use older version of blacklisted regions. Suggest me which genome genome will be better that I can complete my analysis any link or suggestions will be better Thank you

currently I am planing to use mm10 genome from encode the script provided bash download_genome_data.sh mm10 mm10 which will give both reference and blacklisted region

for this I have to realign so.... suggest me any possibility I can get the latest blacklisted regions

Thank you

Answer 1

[ATpoint]

Is v103 the new GRCm39? If so then do yourself a favor and mm10 reference genome. Basically all relevant resources are available for mm10, and probably almost none (so far) for the updated reference genome. Don't make it harder than necessary.

[luckysardar171]

Thank you for the reply.. Okay I will use mm10 from encode.

[ATpoint]

It is just waaaay more convenient, the new reference genome is not yet established enough and I doubt you will gain anything by using it, make your life easy(er) use mm10 indeed.