Question: How analyse chip-exo paired read data and get BigWig or Peaks called?
0
gravatar for morovatunc
2.9 years ago by
morovatunc400
Turkey
morovatunc400 wrote:

Dear all hi,

I have paired end chip-exo data. The interesting is, both reads from each of the pair was already mapped and peaks were called. I have data in BED format which caused a confusion because of the paired end reads. Even though I have found couple softwares for paired chip-exo analysis, they all require bam input. I dont want to do all the alignment again therefore I wanted ask the community of booster.

My aim is to get BigWig file format for visualisation and ~250 bp peaks for the data process(finding overlaps etc.);

1) I am totally lost for the bigwig part so I beg for your information. Can I obtain BigWig with current available information? (I checked bed to BigWig threads from seq answers and biostars but can I solve it with using bedtools genomeconv)

2) For obtaining ~250 bp peaks I thought merging them with bedtools could be a solution. Is there a gold standard for merging process ?

Could you enlighten me a bit. Any document regarding this information would be very useful as well.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43785 — > source of the data.

            Tuncs-MacBook-Pro:~ morova$ more /Volumes/blackhole/chip-exo/GSE43785_RAW/GSM1071284_120424_ChipEXO5_NoIndex_L005_R1.fastq.tagAlign.bed
            chr12   79171842        79171891        -
            chr4    144341449       144341498       -
            chr3    42101448        42101497        -
            chr19   18496785        18496834        +
            chr3    24961259        24961308        +
            chr5    4818754 4818803 +
            chr10   88177242        88177291        +
            chr2    45031538        45031587        +
            chr3    190478599       190478648       +
            chr20   8807491 8807540 -

Thank you for your help,

Best,

Tunc.

bed bedtools • 1.0k views
ADD COMMENTlink modified 2.9 years ago by genecats.ucsc560 • written 2.9 years ago by morovatunc400
1

ChIP-exo data probably won't have 250bp peaks, resolution is much better than ChIP-seq - see fig from Rhee & Pugh: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243364/figure/F1/

ADD REPLYlink written 2.9 years ago by dyollluap300
1
gravatar for Ian
2.9 years ago by
Ian5.5k
University of Manchester, UK
Ian5.5k wrote:

I think you need to remap to get the BAM files (for genomecov). The description for each sample implies that the bowtie mapped reads are included, presumably in GSE43785_RAW.tar (~60Gb). If you have the space it would be worth checking.

ADD COMMENTlink written 2.9 years ago by Ian5.5k

Thank you very much for your reply!

ADD REPLYlink written 2.8 years ago by morovatunc400
1
gravatar for genecats.ucsc
2.9 years ago by
genecats.ucsc560
genecats.ucsc560 wrote:

Hi Tunc, you can indeed convert bed files to bigWig files using a few UCSC utilities. The main ones you will be interested in are the bedItemOverlapCount and bedGraphToBigWig utils. You can find the appropriate pre-compiled binaries for your system here: http://hgdownload.soe.ucsc.edu/admin/exe/

The usage message from bedItemOverlapCount then explains what to do:

$ bedItemOverlapCount             
bedItemOverlapCount - count number of times a base is overlapped by the
    items in a bed file.  Output is bedGraph 4 to stdout.
usage:
 sort bedFile.bed | bedItemOverlapCount [options] <database> stdin
To create a bigWig file from this data to use in a custom track:
 sort -k1,1 bedFile.bed | bedItemOverlapCount [options] <database> stdin \
         > bedFile.bedGraph
 bedGraphToBigWig bedFile.bedGraph chrom.sizes bedFile.bw
   where the chrom.sizes is obtained with the script: fetchChromSizes
   See also:
 http://genome-test.cse.ucsc.edu/~kent/src/unzipped/utils/userApps/fetchChromSizes

If you have any follow up questions, it would be helpful if you could post them to our Google Groups forum: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome, that way our whole team can see the question and help with an answer.

Thanks,

ChrisL from UCSC

ADD COMMENTlink written 2.9 years ago by genecats.ucsc560

Thank you very much for your reply!

ADD REPLYlink written 2.8 years ago by morovatunc400
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