User: colin.kern
colin.kern • 650
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Posts by colin.kern
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... You can see the format specifications here: https://genome.ucsc.edu/FAQ/FAQformat.html#format13
The only difference is the narrowPeak format has one additional column that indicates the peak summit. ...
written 4 days ago by
colin.kern • 650
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Comment:
C: GC bias correction for Chip-SEQ
... The way current sequencing technology works introduces biases for GC-rich areas of the genome, so they tend to get more reads than other areas. This is hard to account for in ChIP-seq because the areas of interest (promoters, enhancers, etc.) often are GC-rich themselves, so the bias is expected bio ...
written 5 days ago by
colin.kern • 650
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Answer:
A: Chip-Seq macs2 peak calling
... The output files are explained in the README. Just go here: https://github.com/taoliu/MACS and look near the bottom of the page for the "Output Files" section. The narrowPeak file is an extension of the BED format, which is why it's used for bedtools.
You are going to have be a lot more specific a ...
written 5 days ago by
colin.kern • 650
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... A raw p-value is in the range 0 to 1, so 19.2 is clearly not a p-value. The narrowPeak and broadPeak formats, which are standard formats for peak calls that are extended from the BED format, represent p- and q-values as -log10 transformed values. The Roadmap data structure is probably derived from t ...
written 5 days ago by
colin.kern • 650
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Answer:
A: Effect of gene size on WGCNA
... Like DEG analysis, WGCNA is looking at each gene independently of one another. All that matters is how the expression of the same gene compares across samples. That comparison will be proportionally the same whether you normalize by gene length or not, because all the values within each comparison a ...
written 6 days ago by
colin.kern • 650
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... Is this data from cell lines or frozen tissue? ChIP-seq can be a very hard assay to get consistent data from, especially with tissue, because there can be very large differences in the signal-to-noise ratio even when following the exact same protocol. Seeing that it is consistently the second replic ...
written 8 days ago by
colin.kern • 650
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... LincRNA means "long intergenic non-coding RNA", whereas lncRNA is just "long non-coding RNA". Many people use them interchangeably. The only scenario I can think of where there might be a lncRNA that's not a lincRNA would be a lncRNA that overlaps a coding gene on the antisense strand, but I have a ...
written 8 days ago by
colin.kern • 650
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... Samtools flagstat reports individual reads, not read pairs. The fragments in Macs2 output is referring to pairs of reads, so that's why you're getting half the number. The 370,935 difference may be Macs2 filtering read pair alignments that are considered "properly paired" in samtools but not by Macs ...
written 8 days ago by
colin.kern • 650
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... It depends on the analysis you're doing. Normalization for gene length isn't done in edgeR or DESeq2 because for DEG analysis you are only comparing counts of the same gene across samples, so normalizing by gene length won't change the proportions of the numbers of the same gene across samples. If y ...
written 8 days ago by
colin.kern • 650
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... Yes, skipZeros removes bins with values of zero in all samples, so it will remove bins in unmappable regions, but if you have just one read in one sample, then that bin is included, so it doesn't help to remove any of your background noise.
TPM's benefit over FPKM/RPKM is well documented in RNA-seq ...
written 11 days ago by
colin.kern • 650
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