Hello All,
I would like to know if there are any specific programs out there that help to identify promoters in PLANTS. Specifically I...
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Promoter Identification programs
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How to decide the side (5' or 3') close to TSS in GTF
Hi everybody
I’d like to ask you about TSS (transcription start site) annotation
Now I’m analyzing Total RNA-seq data by ENCODE... -
Distance to TSS Primer Design
I have what is probably a stupid question, but I'm really not sure what to do. How do people usually use distance to TSS when designing primers for ChIP-qPCR... -
Low mapping rate of TSS-data (5'-seq)
Hi,
We have performed transcription start site sequencing (TSS, 5'-sequencing) using TAP treatment (tap+ and tap- of totalRNA) and Illumina... -
Tuxedo suite not giving alternative TSSs their own loci
Hey,
I am hoping to characterise alternative TSSs in my samples.
I have processed them through to CuffNorm and, although... -
from gene symbols to a BED file with TSS positions
Hi all
I have a list of gene symbols (in excel or txt file) and I would like to get a BED file containing all the TSS positions of that... -
Hi everyone! some questions about TSS
Hi i am new. I just noticed that some papers define the region within 1 kb to TSS as "near TSS: while the region over 1kb as "far away from... -
Get Promoter Sequence for List of RefSeq IDs
Dear All,
I have a list of RefSeq IDs. Each ID consists of a pair of IDs (protein ID;mRNA ID) for example (NP_001135412.1; NM_001141940.1).... -
Unknown definitions of instances output by CummeRbund
Hi all,
Now I am trying to analyze the results of differential expression tests using CummeRbund. I simply loaded the output files of Cuffdiff... -
transcription start sites (TSS)
Hi all!
I'm new to ChIPseq analysis and have a question regarding TSS.
I need to compare my ChIPseq regions against transcription... -
How to get transcript start site by RNAseq data in the vertebrate genome
I am working on a vertebrate genome now and have RNAseq data of several different tissues sequenced by Illumina Hiseq 2000 platform. I have a gene set... -
Transcription start sites clustering
Hello, everybody. I am new here and am working on transcriptional start sites (TSS) identification. Does anybody happen to know a good software to cluster... -
ChIP-Seq reads correlated/distance to with TSS/promoter etc.
Hi all,
Interested in producing some of those plots that illustrate the read density at some distance from the transcription start site,...
