Question: TSS sites of GRCM38
0
gravatar for kanwarjag
10 months ago by
kanwarjag1.0k
United States
kanwarjag1.0k wrote:

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

Thanks

tss chip-seq • 497 views
ADD COMMENTlink written 10 months ago by kanwarjag1.0k
1

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

ADD REPLYlink written 10 months ago by genomax75k

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.

ADD REPLYlink written 10 months ago by kanwarjag1.0k

Use it with what? What was the error?

ADD REPLYlink written 10 months ago by genomax75k

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

ADD REPLYlink modified 10 months ago • written 10 months ago by anshupa.vssut50
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