Human vs. Mice Step 3. Fragments-in-promoter ratio

[EDYAC]

Hello, If Im using Human genome, will the promotor file provided in step 3 work or I need a human promoter.bed file? Also Is this a necessary step? can I move to step 4 without going through step 3? Thank you

[r3fang]

If it’s 10X data I recommend to run this step but if you just want to run through the pipleline, you can skip this step and get the cluster

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On May 13, 2019, at 2:50 PM, BrainEmpty notifications@github.com wrote:

Hello, If Im using Human genome, will the promotor file provided in step 3 work or I need a human promoter.bed file? Also Is this a necessary step? can I move to step 4 without going through step 3? Thank you

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[EDYAC]

it's actually 10X, so it's the same thing regardless of being human or mice genome?

[r3fang]

No the list for human and mouse is different

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On May 13, 2019, at 2:58 PM, BrainEmpty notifications@github.com wrote:

it's actually 10X, so it's the same thing regardless of being human or mice genome?

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[EDYAC]

Any suggestions? where to get it from?

[r3fang]

You can download from UCSC genome browser. They have an option to download promoter 2kb upstream of tss.

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On May 13, 2019, at 6:29 PM, BrainEmpty notifications@github.com wrote:

Any suggestions? where to get it from?

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[EDYAC]

Hi, I'm having a hard time finding the promoter list you are talking about, Would you be able to help please?

[r3fang]

use this one:

http://renlab.sdsc.edu/r3fang/share/Fang_2019/published_scATAC/atac_v1_pbmc_10k_fastqs/hg19_promoter.bed