Running the wrapper - bed.gz files?

[joshcutts]

Thanks so much for writing this wrapper. Thanks to your previous help I've got everything successfully installed and can run the example that you included for chr 21.

At this point I'm just a little confused on how to get things running with my files. I see that you included a couple of gzipped bed files and it looks like your wrapper will create the input files (3 columns with counts from these bed files? (I see this file in the output along with the enhancer predictions) I just want to ask what exactly are these bed files? Are these peak files? Or bam alignment files that have been converted to bed? Would it be possible to use bam files directly?

Thanks!

[kaizhang]

The bed files should contain aligned tags. You can get them from bam files using bedtools. It's currently not possible to use bam files directly.

[joshcutts]

Thanks so much I really appreciate it! Just one more question - does the wrapper take care of the RPKM normalization or is that something I should be taking care of in generation of the bed files?

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On Wed, Feb 6, 2019 at 11:19 AM Kai Zhang ***@***.***> wrote: The bed files should contain aligned tags. You can get them from bam files using bedtools. It's currently not possible to use bam files directly. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Abox4crXBv-DzqMnEgEnW-zTUKk6TOobks5vKxyggaJpZM4aiWUr> .

[kaizhang]

It takes care of the normalization. You just need to provide the aligned tags.