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guanjue / IDEAS_2018

Jointly characterizing epigenetic dynamics across multiple cell types
MIT License
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Averaging Replicates #13

Closed YogiOnBioinformatics closed 2 years ago

YogiOnBioinformatics commented 2 years ago

Hello @guanjue,

Hope you're well!

I wanted to clarify the instructions for the prepMat regarding replicates as stated here: https://github.com/guanjue/IDEAS_2018/blob/5881efae8e42ce711766d021a88e2cfe309a1f52/IDEAS_APP/readme_prepMat#L32

How exactly do I average the files?

Can I assume the 1 millionth line in ATAC_rep1.bed.gz corresponds to the same region as the 1 millionth line in ATAC_rep2.bed.gz? The above assumes I've used the prepMat program to create the files.

If the answer is "yes" to my above question, I guess I could just iterate through each line in the .bed.gz files for a group of replicates and take the average. (i.e. take line 1 from 3 different replicate .bed.gz files and average these 3 numbers all from line 1 of the original file)

YogiOnBioinformatics commented 2 years ago

@guanjue

Apologies, don't mean to bother. Just wanted to follow up on this.

guanjue commented 2 years ago

Hi,

Sorry, for the late reply.

For Q1, the answer is yes. For each row, it will be a 200bp bins' read counts for each replicate of each epigenomic feature. So, yes, you can simply take the row-means as the average.

Best wishes. Guanjue

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Apologies, don't mean to bother. Just wanted to follow up on this.

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YogiOnBioinformatics commented 2 years ago

Awesome, thanks so much!