HINT Footprinting analysis for ATAC-Seq
Hi everyone,
I am new at ATAC-Seq data analysis, and I have a few questions. I apologize in advance if these questions are basic, and/or if I am using the wrong syntax in these questions.
1) I have run F-Seq on bed files, which generated wiggle and npf files. Several of each type. What do these files represent? In other words, what do I do with them?
2) I intend to run HINT footprinting analysis. I read through some of the tutorials online, but I'm still unclear on the input. Do I use the bam and bed files that I used for F-Seq? Or do I somehow use the output from F-Seq as input for HINT? Pardon if this question doesn't make sense. Any clarity will help.
Thanks in advance!
I am new at ATAC-Seq data analysis, and I have a few questions. I apologize in advance if these questions are basic, and/or if I am using the wrong syntax in these questions.
1) I have run F-Seq on bed files, which generated wiggle and npf files. Several of each type. What do these files represent? In other words, what do I do with them?
2) I intend to run HINT footprinting analysis. I read through some of the tutorials online, but I'm still unclear on the input. Do I use the bam and bed files that I used for F-Seq? Or do I somehow use the output from F-Seq as input for HINT? Pardon if this question doesn't make sense. Any clarity will help.
Thanks in advance!