User: dcheng1

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dcheng10
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Posts by dcheng1

<prev • 7 results • page 1 of 1 • next >
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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 4 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 4 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 12 months ago by dcheng10 • updated 12 months ago by WouterDeCoster29k
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Comment: C: Problems with MACS ChIP-Seq peak calling
... Link for igv screenshot: https://ibb.co/dXZhvv ...
written 12 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 12 months ago by dcheng10 • updated 12 months ago by YaGalbi1.3k
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Comment: C: how to find the primer for the promoter of VEGF gene?
... very helpful!Thanks!! ...
written 20 months ago by dcheng10
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how to find the primer for the promoter of VEGF gene?
... Hi, I want to determine the expression level of VEGF-A by ChIP-qPCR, as active h3k4me3 are positively related with VEGF-A expression. the promoter regions of VEGF-A is usually highly methylated at h3k4. So I need to design a primer that covers the promoter regions of VEGF-A. Does anyone know how to ...
vegf chip-qpcr primer design written 20 months ago by dcheng10 • updated 20 months ago by natasha.sernova2.9k

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