TSS sites of GRCM38

Question

[kanwarjag]

How can I get TSS file (bed/ GTF) for GRCM38? I can see mm9 file but not GRCm38

Thanks

[GenoMax]

https://ccg.epfl.ch//mga/mm10/ucsc/ucsc.html

[kanwarjag]

I tried to use the above TSS file but it is not compatible with GRCM38 and giver error that ist column annotations-NC.... can not be recognized.

[GenoMax]

Use it with what? What was the error?

[anshupa.vssut]

Did you try the following in R?

library(GenomicFeatures)
chromInfoDF <- read.table("chrNameLength.txt")
chromInfoDF <- data.frame(chrom = chromInfoDF[,1], length = chromInfoDF[,2], is_circular = chromInfoDF[,1] == "MT")
txdb <- makeTxDbFromGFF(file = "Mus_musculus.GRCm38.83.gtf", format = "gtf", dataSource = "Ensembl 83", organism = "Mus musculus", chrominfo = chromInfoDF)
tss = promoters(txdb, upstream = 1500, downstream = 1500, columns = c("tx_name", "gene_id"))

NOTE: chrNameLength.txt file has two columns: chromosome number and length of chromosome, you can export the tss object as bed