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Recent Replies
Comment: Generating consensus sequence from bam file
by
a1ultima
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760
Hey @genomax , it worked after I just put the ref.fa after the -Oz flag
Answer: How to produce a heatmap by keeping the original data and a log color scale?
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anikcropscience
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Anyways, the problem is solved by using breaks. Thank you.
Comment: Bioinformatics tutor good in Python
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Good evening Sir, I have already emailed you.
Looking forward to your reply.
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Comment: different sequencing depths for Input and IP in ChIP-Seq
by
Genestar
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Thank you both for your suggestions. I will try both the approaches and see what works best.
Comment: Seurat - setting random seed for FindNeighbors, FindClusters
by
bsmith030465
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The 'random.seed' argument has been passed into the 'FindClusters' function (see code in post). However, there doesn't appear to be any suc…
Comment: different sequencing depths for Input and IP in ChIP-Seq
by
ATpoint
49k
If you are ok with omitting the inputs then you can normalize the IPs using https://www.biostars.org/p/413626/#414440 to get scaled bigwigs…
Comment: different sequencing depths for Input and IP in ChIP-Seq
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Carlo Yague
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Even so the SES method above should work well for visualization and in particular if you want to look at each IP-input heatmap separately. …
Comment: different sequencing depths for Input and IP in ChIP-Seq
by
Genestar
•
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Apologies, if I was not clear. I do have multiple IP samples, each with a corresponding Input sample. Just the Input samples were sequenced…
Comment: different sequencing depths for Input and IP in ChIP-Seq
by
Carlo Yague
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Probably not, IMHO the SES method is more like a "within sample" normalization (IP - input of the same sample). From what I read of the OP,…
Comment: different sequencing depths for Input and IP in ChIP-Seq
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ATpoint
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Does that ensure comparability between IPs, e.g. what TMM from edgeR is doing, so correcting for compositional differences between librarie…
Answer: different sequencing depths for Input and IP in ChIP-Seq
by
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Before normalizing the IP to the input (input subtraction I guess), I recommend using the [signal extraction scaling (SES)][1] method, whic…
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9 years later...has this here ever come to a working solution? I wonder how, despite all the modeling approaches, you address the compositi…
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You can try [this script][1] to see you can get a BED format file (which is what you are describing).
[1]: https://gist.github.com/bran…
Comment: different sequencing depths for Input and IP in ChIP-Seq
by
Genestar
•
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Hi, its just to plot a heatmap of the IP normalized to the Input.
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Lila M
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Exactly, I want to know if there is any homology in my regions or around the breakage sites. This is why I asked for clarifications before,…
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