How to annotate probe to nearest gene promoter?

Question

[BioNoobie]

I have DrIP-Seq data, I have aligned it to human, and with the mapped bam, we have used Seqmonk to get the peak value (define probe- MACS peak caller, by read count), after we got the peak, we tried to annotate the peak to the nearest gene. We tried with the closest to gene/CDS/mRNA also with upstream/downstream to gene/CDS/mRNA

After annotation, the peak annotated nearest to the negative-strand upstream is not upstream of the gene but in the end of the last exon. Is there any better way to annotate these with the proper promoter region?

Thanks

[Trivas]

I would create a custom bed file where you shift the start upstream by about 1000 nt, and the stop to be downstream of the annotated TSS by about 100nt. This would allow you to use something like bedtools closest.

[Matthias Zepper]

Give Homer's annotatePeaks a try: It is quite user-friendly and can work with user-provided GTF files.

[BioNoobie]

Hey

Thank you so much, this worked perfectly.