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Comment: ATAC-seq troubleshoot - Just Noise
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ATpoint
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Yes, definitely lots of noise and few peaks for such an experiment. Which celltype is that, and which lab protocol did you use?
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What do you mean by gene lists?
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You can use e.g. the WGCNA package for network analysis. In your case multiple samples this might mean multiple patients or a time series o…
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Thank you so much for your responses.
@genomax , I've downloaded both of the databases you recommended. I attempted to combine them into …
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I think you could try doing this, but it wouldn't be appropriate. You'd be bringing long-read errors, which I believe are higher than short…
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I opened tow terminals and one was the code to build a decoy-aware transcriptome and the other was building indexes (no decoy)
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Thank you for the explanation! So just want to confirm one control with replicate is totally useless even can't use as a reference?
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Comparing samples between labs is a bad idea. Better to generate gene lists from one study from one lab, and gene lists from another study…
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If a sample wasn't prepared along side your treated samples, it is a different batch. If you had treated and controls in each of two diffe…
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You don't need sleuth. Typically these deconvolutions, or most downstream analysis, is done on the gene- rather than the transcript-level w…
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If the top $CPU column shows some values in the hundreds then it is doing something (actually when it's > 0%). So based on the screenshot i…
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Thank you. Waiting it's not gonna hurt me, when should I stop hoping and give up is the question? do you know is there a way if I can see i…
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I divided my contigs using R, but it was more complex than the program Pierre Lindenbaum made (https://jvarkit.readthedocs.io/en/latest/Vcf…
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Just wait until it is finished. It's seems to be running. I just checked my logs and on our HPC with four cores such as process for a decoy…
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