Clarification on the 'null.bed' file in the script

[luckyvivi]

Hello,

I was reviewing the script in your repository and I came across a line where null="null.bed" is assigned. I'm trying to understand the purpose of this file and whether it needs to be created beforehand or if it's a placeholder representing the absence of the H3K27ac mark. Could you please clarify this for me?

Here's the specific line I am referring to:

Thanks in advance.

[liangliangibp]

null.bed is an empty file, you need to create this empty file in advance.

[luckyvivi]

null.bed is an empty file, you need to create this empty file in advance.

Thanks for your response! Creating null.bed in advance works for me.

I also encountered another issue while using your script. I noticed that the promoter region final defined by the script seems to lack strand information. Could you please tell me whether this is by design, or if there might have been a step I overlooked during the process?

[liangliangibp]

We defined the promoter region as the DNA region, and the promoter RNA we considered was transcribed bidirectional, so the positive and negative strand transcripts in this region in our script would be retained for subsequent interaction analysis.

[luckyvivi]

We defined the promoter region as the DNA region, and the promoter RNA we considered was transcribed bidirectional, so the positive and negative strand transcripts in this region in our script would be retained for subsequent interaction analysis.

Thank you for your response. By the way, could you please share the hg19 enhancer and promoter BED files as defined in your article? I would like to compare them with my own to guarantee that there are no inconsistencies in my analysis when executing your scripts.