[Bioc-sig-seq] ChIP-seq analysis in normalization/peak calling between sample and control
Chen-Yi Chen
ChenYiChen at lbl.gov
Mon Mar 29 23:52:06 CEST 2010
Hi Jose,
I tried to use our AlignedRead object feeds into mappedReads2Nhits function from CSAR library, but it returned with an error:
> ChIPnhits = mappedReads2Nhits(ChIPRead, "ChIPnhits_test", chr, chrL)
Error in input$Nhits : $ operator not defined for this S4 class
I believe we don't have "Nhits" column when we read the aligned output from ShortRead, since we are using Bowtie alignment. So here's my question, what does "Nhits" in here means? I believed I need to know what this mean in order to do a custom format read-in for "loadMappedReads."
Thanks!
-Charlie-
----- Original Message -----
From: "Muino, Jose" <jose.muino at wur.nl>
Date: Saturday, March 27, 2010 2:43 am
Subject: RE: [Bioc-sig-seq] ChIP-seq analysis in normalization/peak calling between sample and control
To: Chen-Yi Chen <ChenYiChen at lbl.gov>, bioc-sig-sequencing at r-project.org
> Hi Charlie,
> CSAR package has their own function to load the mapped read files
> (loadMappedReads). Although, it is also compatible with the class
> AlignedRead from ShortRead package; you can directly use an
> AlignedRead object as input on the mappedReads2Nhits function. Let
> me know if it doesn´t work for you
>
> Most likely the problem with the output wig file is that the
> chromosome names used by the genome browser (eg: chr1,chr2
) is
> different to the chromosome IDs of the fasta file that you were
> using to map the reads.
> If you are using the last version (0.99.4), the easy way to change
> chromosome names is in the output of ChIPseqScore. Eg:
> R> test <- ChIPseqScore(control = nhitsC, sample = nhitsS,file =
> "test", times = 10000)
> R> test$chr<-as.character(c(chr1,chr2))
> R> score2wig(test, file = "test.wig", times = 10000)
>
> Let me know if you have any problem.
> Jose
>
>
>
> -----Mensaje original-----
> De: bioc-sig-sequencing-bounces at r-project.org en nombre de Chen-Yi
> ChenEnviado el: vie 26/03/2010 23:02
> Para: bioc-sig-sequencing at r-project.org
> Asunto: [Bioc-sig-seq] ChIP-seq analysis in normalization/peak
> calling between sample and control
>
> Hi all,
> After going through all the ChIP-seq pipeline in ht-seq, I finally
> come down to normalization/peak calling. Interestingly, ht-seq
> seems to not have a standard normalization and peak calling
> algorithm between sample and control. I've read through the
> previous threads about "peaks calling," and people suggest all
> different things.
> So I've tried the following packages:
> chipseq -> using the cutoff as island/peaks calling, and there is
> nothing about normalization technique. From my understanding, I
> thought we need a normalized data from sample and control in order
> to do this, and I certainly don't know how to normalize them in ht-
> seq.SPP -> didn't work, it returned a NaN out of range error when
> doing the enrichment (peak calling) calculation.
> CSAR -> didn't seem to be available in installation through
> biocLite, but I downloaded and installed it manually. It didn't
> seem to work well with ShortRead. (at least I have no idea how to
> do it), and again, wig file output didn't visualize on UCSC genome
> browser.ChIPseqR -> I didn't go in to it that much, but it seemed
> to be the "simulating package"
> ChIPsim -> similar story as ChIPseqR
> PICS -> I visited their website and they mentioned it should be
> available through bioconductor website, but I didn't see any PICS
> packages on bioconductor website.
>
> Is there a standard (or simple) normalization technique/peak
> calling package in ht-seq that we can use?
> I am not a statistician, so any suggestions on this
> normalization/peak calling would really help our analysis.
>
> Thanks a bunch!
>
> -Charlie-
>
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