Question: Finding TSS on genome
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gravatar for sajadmulk000
3 months ago by
sajadmulk0000 wrote:

Hi everyone, can anybody tell me how to find the TSS (Transcription start site) in a Histone modification data for a specific cell taken from the REMC 2015 databank. Thanks in advance.

ADD COMMENTlink modified 3 months ago by toralmanvar750 • written 3 months ago by sajadmulk0000
2

Your question is unclear. Histone modification data indicate ChIP-seq so proteins-DNA interaction, but TSS refers to transcription. What data you you have and what is the final goal? Please be as specific as possible.

ADD REPLYlink written 3 months ago by ATpoint14k

Sorry brother it's the tag i think that make it unclear, i will change that.... thanks for your correction.

ADD REPLYlink written 3 months ago by sajadmulk0000

What is

a Histone modification data

ADD REPLYlink written 3 months ago by WouterDeCoster37k

No, I did not even look at the tags. What confuses is that you indicate to have ChIP-seq data (histone modification), but look for TSS (which implies RNA-seq or related data). What kind of data do you have, so precisely, which experiment?

ADD REPLYlink written 3 months ago by ATpoint14k

want to predict gene expression from the chip data with the help of histone modification that are already done on the DNA strand, transcription starts from TSS , i want to know where to to find the TSS in the chip data.

ADD REPLYlink written 3 months ago by sajadmulk0000
1

Sorry to day but in its current form, your question simply makes no sense at all. There is no TSS in ChIP-seq data. ChIP-seq identifies the binding of the protein or aminoacid modification that you target with an antibody. Please google chromatin-immunoprecipitation. What you can do is to check if a region carries histone modifications that are associated with active transcription like H3K4me3 or H3K9ac, but this is only a hint that transcriptional events may happen in this area. If language barrier is a problem here, also feel free to link a publication or an article/website that has already done the kind of analysis you are looking for so that we can better understand what you actually want to do.

ADD REPLYlink written 3 months ago by ATpoint14k

thanks for your appreciation. where / how to find TSS of gene in this here for a specific gene.

ADD REPLYlink written 3 months ago by sajadmulk0000

Do you want to identify TSS from ChIP data? That cannot be done without a lot of different ChIP data.

ADD REPLYlink modified 3 months ago • written 3 months ago by kristoffer.vittingseerup1.6k

where / how to find TSS of gene in this here for a specific gene.

ADD REPLYlink modified 3 months ago • written 3 months ago by sajadmulk0000

The TSS is the beginning of the transcript, which in humans is quite well annotated and doesn't require ChIP information (you could use it to infer which TSS is likely being used, but if you already have RNA-seq there's no reason to bother. For PAX5 in hg19, the three TSSes are around 37034500, 37026500, and 37002800.

ADD REPLYlink written 3 months ago by Devon Ryan88k
0
gravatar for toralmanvar
3 months ago by
toralmanvar750
toralmanvar750 wrote:

I am not able to understand your question properly, but if you mean annotating the peaks obtained from ChIP-Seq for histone modification study. Then you can try using annotatePeaks.pl which is a simple perl script, a part of HOMER package. You basically need 3 files for running it:

Peak bed file
reference genome fasta file
reference genome annotation (gtf/gff) file

And command goes like this:

perl annotatePeaks.pl sample_peak.bed Genome.fasta -gft genome.gft >homer_annotation.txt

It basically gives you "Distance to the nearest TSS".

For other alternatives, you can go through this post.

ADD COMMENTlink written 3 months ago by toralmanvar750

where / how to find TSS of gene in this here for a specific gene.

ADD REPLYlink modified 3 months ago • written 3 months ago by sajadmulk0000
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