User: Pappu

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Pappu1.9k
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Posts by Pappu

<prev • 416 results • page 1 of 42 • next >
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genomic region haplotype
... I am wondering if there is any quick way to identify if a list of genomic regions or SNPs lie in the same haplotype. ...
snp written 8 weeks ago by Pappu1.9k
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Peak length for TF motif discovery
... I noticed several possibilities of using the whole peak fasta sequence, 100 or 250bp up and downstream of peak midpoint for motif discovery in MEME or HOMER. I am wondering what is the standard protocol for this. The same goes for selecting background sequences - should it come from shuffling the pe ...
chip-seq written 8 weeks ago by Pappu1.9k • updated 8 weeks ago by khorms210
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Comment: C: Pooling replicates for CHIP-seq peak calling
... I agree. I saw pooling of 2 control replicates for peak calling in MACS2. ...
written 9 weeks ago by Pappu1.9k
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Pooling replicates for CHIP-seq peak calling
... I am wondering what is the difference between pooling 2 replicates and 2 IGG controls for ChIP-seq peak calling compared to running the peak calling separately and doing IDR to integrate the peaks. ...
chip-seq written 9 weeks ago by Pappu1.9k • updated 5 days ago by Biostar ♦♦ 20
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Genome region annotation
... I am wondering which tool is good for annotating human genome regions like Genes, Promoters etc which takes into account overlapping genes. ...
next-gen chip-seq written 9 weeks ago by Pappu1.9k
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Comment: C: ChIP-seq Motif Enrichment
... I got that. How do you derive a p-value from that if say 30% sequences have that motif? ...
written 9 weeks ago by Pappu1.9k
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Comment: C: ChIP-seq Motif Enrichment
... Thanks. I was thinking about MEME-ChIP. ...
written 9 weeks ago by Pappu1.9k
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Comment: C: ChIP-seq Motif Enrichment
... In other words, how can one check if the TF is binding to the right places in the genome based on a known TF binding motif from TRANSFAC? ...
written 9 weeks ago by Pappu1.9k
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ChIP-seq Motif Enrichment
... I am wondering what would be the idea way to carry out motif enrichment analysis from ChIP-seq data in order to see that the peaks called are significantly enriched for a TF motif compared to other regions in the genome. ...
chip-seq written 9 weeks ago by Pappu1.9k
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How to do ChIP-seq QC
... I am wondering what are the QCs for a TF ChIP seq in order to make sure the experiment or antibody worked properly. One way to check the percentage of peaks occurring near the promoter regions. What are other standard ways to check it? ...
chip-seq written 9 weeks ago by Pappu1.9k • updated 9 weeks ago by jared.andrews078.3k

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