User: dcheng1

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dcheng10
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Posts by dcheng1

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Comment: C: Macs called peaks shorter than 1kb
... I just realized for the above shown data, the reads is only 2 million. Below is another data with 6 million reads: ![enter image description here][1] [1]: https://i.postimg.cc/XNK28MRt/igv_snapshot-6.png ...
written 11 weeks ago by dcheng10
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Comment: C: Macs called peaks shorter than 1kb
... I think you're correct, the signal track is for fold change. I used AQUAS chip-seq pipeline to get this bigwig file.(https://github.com/kundajelab/chipseq_pipeline) Below is the snapshot for the BAM file and fc bw file opened in the IGV: ![enter image description here][1] [1]: https://i.postim ...
written 11 weeks ago by dcheng10
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Comment: C: Macs called peaks shorter than 1kb
... ![enter image description here][1] [1]: https://i.postimg.cc/jqHjgB1N/igv_snapshot.png ...
written 12 weeks ago by dcheng10
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Comment: C: Macs called peaks shorter than 1kb
... Yes, H3K4me3 peaks are narrow. However I usually observed peaks with average length 2kb in high quality data. The short peaks(~700bp)look like spikes, not bell curved shapes. ...
written 12 weeks ago by dcheng10
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Macs called peaks shorter than 1kb
... For ChIP-seq data of H3K4me3 histone modification. I used MACS2 to call peaks with default setting. However I identified a large number of peaks with length below 700bp. Those peaks look like vertical bars in IGV. Any opinions are greatly appreciated!! Below is a subset of the narrowPeak file: ...
chip-seq written 12 weeks ago by dcheng10 • updated 12 weeks ago by benformatics350
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Comment: A: MACS2 gives negative estimated fragment length
... I target histone modification H3K4me3. I used AQUAS chipseq pipeline, so I didn't type in any macs2 command, but I think the command is: callpeak -t -c -f BED -n -g hs -p 0.01 --nomodel --shift 0 --extsize 345 --keep-dup all -B --SPMR ...
written 9 months ago by dcheng10
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MACS2 gives negative estimated fragment length
... Hi, I have two ChIP-seq replicates and their peak profile looks very similar in genome browser. When I use macs2 to call peaks, rep2 has a 345 bp of estimated fragment length, but the est. fragment len. of rep1 is -5. I wonder how this happened since these two replicates seems to correlates with e ...
chip-seq written 9 months ago by dcheng10
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Comment: C: Problems with MACS ChIP-Seq peak calling
... track type=bedGraph name="NA_treat_all" description="Extended tag pileup from MACS version 1.4.2 20120305" chr1 10002 10003 1 chr1 10003 10004 2 chr1 10004 10008 3 chr1 10008 10014 4 chr1 10014 10015 5 chr1 10015 10016 7 chr1 10016 10020 8 chr1 10020 10021 9 c ...
written 18 months ago by dcheng10 • updated 18 months ago by WouterDeCoster35k
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Comment: C: Problems with MACS ChIP-Seq peak calling
... Link for igv screenshot: https://ibb.co/dXZhvv ...
written 18 months ago by dcheng10
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Problems with MACS ChIP-Seq peak calling
... I downloaded raw data in GEO and analyzed it following general ChIP-Seq pipeline: trimming adapter, mapping and calling peaks. However, when compared with bigwig files in GEO, my results look like separate spikes instead of peaks. Here is the command I used: macs14 --bw 200 -t -c -B -S --call-su ...
macs peak calling chip-seq written 18 months ago by dcheng10 • updated 18 months ago by YaGalbi1.4k

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