Closed Ying-Lab closed 2 months ago
Hi,
To achieve your goal, the window
subcommand of bedtools should be useful.
Here’s an example command:
bedtools window -a $A_Bed -b $B_Bed -w $width
In this command:
$A_Bed
represents a cell-type-specific TF ChIP-seq BED file that you can download from Peak Browser.$B_Bed
is a BED file containing the transcription start sites (TSS) of all genes.$width
specifies the distance range from the TSS, for example, 5000.You can obtain the appropriate $B_Bed
files (originally sourced from the UCSC Genome Browser) from here. Please feel free to reach out if you need any further assistance.
BR, Zhaonan
Thank you so much! I tried the pipeline and it worked well.
Hi there!
Thanks for the excellent work!
I am interested in getting the cell-type-specific TF-gene regulations. However, in the taget gene module, I find that all the potential target genes are provided for a certain TF. In the Peak-Browser, the cell-type-specific TF ChIP-seq bed file can be downloaded. I tried to process the bed file via annotatePeak function of ChIPseeker package, while some errors always ocurred,indicating that 'start' or 'end' cannot contain NAs.
Therefore, I was wondering if there is a more convenient way to get the cell-cell-specific TF-gene regulations according to all the cell-type-specific ChIP-seq data?
I look forward to your reply. Thanks in advance for your time and help!
Best, Scotty