Hello Guys,
I have analyzed a set of ChiP-seq data for a Transcription factor. I have my BigWig files and a list of genes names (ncRNA)...
29 results in 0.0030 seconds.
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How do I convert a list of ncRNA genes into annotation using UCSC table browser
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BedTools Fisher Question
Hi, All! I have a question about the usage of the bedtools fisher tool. I have posted elsewhere but have not received answers.
I am trying... -
ChIPSeq sequencing depth for histone modifications
Hi,
We would like to sequence mouse Histone modification (H3K4me3,H3K4me1,H3K27me3,H3K27ac) chip-seq samples using illumina Hiseq2500. Previously... -
Stuck at adapter trimming
Hi!
So, I'm trying to analyse and subsequently map the data deposited with the following paper:
http://science.sciencemag.o... -
MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
Dear Community,
Please take a look at MicroScope: https://bmcbioinformatics.biomedcent...859-016-1260-x
...Last edited by Bohdan_Khomtchouk; 09-23-2016, 10:13 AM. -
ChIP-Seq knockouts v. inputs - how to analayze my data?
My data is actually RIP-Seq (RNA immunoprecipitation). However, I don't feel I am getting the answers I need asking around from an RNASeq perspective....Last edited by syntonicC; 09-13-2016, 06:52 AM. -
ChIP-seq and Peak calling
I have a simple question that I would like some opinions on. If a transcription factor is highly expressed (protein) in one cell and say now that the... -
htseq-count failure parsing GFF attribute line
Hi,
I am trying to generate a read counts file for my ChIP-seq data using htseq-count. Here is what I have done so far:
1. Call... -
Finding significantly different ChIP-seq peak length?
Hello,
I have a simple data analysis question.
Say I have a protein ChIP-seq data comparing three replicates of wild-type... -
Finding Overlapping Regions of Chip-Seq results, then visualising it.
Hi,
I am trying to visualise my overlapped chip-seq peak regions which I analysed with Homer mergePeaks function. I have got one venn info... -
MACS: ChIP and control with different tag size
Hi,
I am using MACS2 for ChIP-seq peak calling.
I have a treatment file with original reads of 51bp. Before alignment, the reads... -
Input giving peak at TSS! Yikes!
Hi all,
It's my first attempt at ChIP-seq. I optimized fixation time, shearing, IP. I confirmed my ChIP was working by qPCR. Prepped libraries... -
Which software/algorithm do you use to find DMR in chipseq methylation data?
I'm fairly new in the CHIP-seq field and would like to have recommendation on the best way to find DMRs.
Which software/platform/algorithm... -
Chip-seq publicly data for download ?
Hello all,
could anyone suggest me ? how and where to download publicly Chip-seq data-sets for medicinal plants ??
Need to work... -
CexoR: peak-pair calling in ChIP-exo data with replicates
Dear bioinformatics community,
If you are producing of analyzing ChIP-exo data (Rhee HS, Pugh BF, 2011, Cell 147:1408-19) with replicates,...
