User: science_lizard

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Posts by science_lizard

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Comment: C: how to format the featurecounts output ?
... Can you post the code you used and which SAF or GTF you used? Did you make the SAF yourself? ...
written 16 days ago by science_lizard0
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Extend ChIP-seq peaks to known Restriction Enzyme Digest Sites?
... I am performing a protocol that is very similar to ChIP-seq, except that it uses restriction enzyme digestion (with a cocktail of 4-5 restriction enzymes) rather than regularly-spaced MNase digestion or sonication. This presents some difficultly when peak calling, as the peaks will be a mixture of ...
peak calling macs2 chip-seq homer written 21 days ago by science_lizard0
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Comment: C: Is it acceptable to use different FDR cutoffs for peak calling in different ChIP
... That's kind of what I was thinking but I wanted to make sure this wasn't breaking some cardinal rule of peak calling. Thank you!! ...
written 23 days ago by science_lizard0
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Is it acceptable to use different FDR cutoffs for peak calling in different ChIP-seq experiments (with same antibody)?
... This is more of a statistics question, but I'm wondering if you think that it's acceptable to use different FDR thresholds for peak calling in one experiment vs. another with the same antibody. I have some ChIP files (this is actually not ChIP, but it's a protocol very similar except that I use res ...
fdr peak calling chip-seq homer statistics written 26 days ago by science_lizard0 • updated 25 days ago by benformatics1.8k
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Comment: C: Correlate ChIP-seq to gene expression
... Ohhh, yeah annotation totally makes sense here, thank you! This completely clarifies it!! ...
written 29 days ago by science_lizard0
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Comment: C: Correlate ChIP-seq to gene expression
... Thanks, this makes sense. So to be clear, then do you mean I would use FeatureCounts on my ChIP-seq data so that I can get the coverage across genes? I can't think of another way to do it, since I imagine the scatterplot would require the same genomic ranges/genes for the X and Y axes, is that corre ...
written 29 days ago by science_lizard0
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Comment: C: Correlate ChIP-seq to gene expression
... Thanks for your reply! So if I'm understanding what you mean, I think I've done that kind of analysis before. Annotated my ChIP-seq peaks with different thresholds (e.g. 300 bp from TSS, 1000bp from TSS etc), but where I get a little confused is how to combine the ChIP data with the RNA counts. If I ...
written 4 weeks ago by science_lizard0
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Comment: C: STAR multiple FASTQ alignment, can you use with a variable $?
... Thank you! Yeah the ${FASTQ1},${FASTQ2} doesn't work either, it's something about having the comma right between the two variables makes it break down when using a wildcard. But I'll give the other options a shot, thanks! ...
written 4 weeks ago by science_lizard0
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Correlate ChIP-seq to gene expression
... I'm looking for a way to compare ChIP-seq signal to gene expression, and not 100% sure the best way to do this. To be specific, the end goal is to make a scatter plot with (normalized) RNA-seq counts on the X-axis and (normalized) ChIP-seq on the Y, and calculate a correlation coefficient. I have ...
chip-seq featurecounts correlation counts rna-seq written 4 weeks ago by science_lizard0 • updated 29 days ago by rohitsatyam102170
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Answer: A: RNA-seq and histone modifictaion
... You can peruse this database for your desired dataset: https://www.encodeproject.org/search/?type=Target Also I've never used it before but I hear this is also a good place to look: https://deepblue.mpi-inf.mpg.de ...
written 4 weeks ago by science_lizard0

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