User: Lucy

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Lucy0
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Posts by Lucy

<prev • 15 results • page 1 of 2 • next >
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Error with fitCentipede
... Hi, I am getting the following error when I run fitCentipede on my data: Error in quantile.default(Rlist[[1]], 0.9) : missing values and NaN's not allowed if 'na.rm' is FALSE Calls: ... eval -> fitCentipede -> quantile -> quantile.default Does anyone know what the cause of this is an ...
R centipede written 11 days ago by Lucy0
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CENTIPEDE - values from fitCentipede
... Hi, Is there somewhere that gives detailed information about the different values output by the fitCentipede function in the CENTIPEDE package? I have run CENTIPEDE on my ATAC-seq data, but now that I have the output, I am not sure what to do with it. How do I know if they are confident in which ...
R atac-seq centipede written 18 days ago by Lucy0
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featureCounts - how to make ATAC-seq cut-sites BAM
... Hi, I am trying to calculate the cut sites for my ATAC-seq data and then use these for featureCounts. However, I am unclear exactly how to write the cut sites in BED file format. I have made two different BED files. In the first, I modified the start and stop position for all forward (+) reads t ...
featurecounts bed files written 5 weeks ago by Lucy0 • updated 5 weeks ago by genomax58k
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Comment: C: featureCounts allowMultiOverlap - fractional or not?
... Thank you - I am now trying to perform featureCounts with the cut sites instead. ...
written 5 weeks ago by Lucy0
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Comment: C: When using MACS2 with -f BAM, it is possible to have a shift other than 0?
... Thanks for the message. I think I have decided to go with -f BAMPE and no shifting. ...
written 6 weeks ago by Lucy0
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featureCounts allowMultiOverlap - fractional or not?
... Hi, I am running featureCounts on my ATAC-seq data. I have allowed multi-overlapping reads (i.e. reads that overlap with more than one peak). However, I am unsure whether to include the --fraction option (assign fractional counts to features) or whether I should allow each overlap to count as 1. ...
featurecounts atac-seq written 6 weeks ago by Lucy0
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FRIP score ATAC-seq
... Hi, I am trying to calculate the fraction of reads in peaks (FRIP score) for my ATAC-seq samples. What I have so far is written below, however I think it is wrong somehow as I am getting a very low score (when I calculate the FRIP using DiffBind, it comes out much better/more like the expected val ...
frip atac-seq written 8 weeks ago by Lucy0 • updated 7 weeks ago by chaton0
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Comment: C: Determine peak summits after IDR analysis
... Thank you. Please could you explain the first part in more detail. I would take column 10 from my .narrowPeaks file, which is the relative summit position and place this into the fifth column of which file? ...
written 8 weeks ago by Lucy0
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Comment: C: Determine peak summits after IDR analysis
... macs2 was used for the initial peak calling ...
written 8 weeks ago by Lucy0
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Determine peak summits after IDR analysis
... Hi, I have performed ATAC-seq on three different cell subsets and have generated an optimal peak list for each using IDR analysis. I then ran bedtools merge to generate a global peak list for all of the subsets combined. However, by merging the peaks, I lose the summit information i.e. some peaks ...
peak summits macs2 idr written 8 weeks ago by Lucy0 • updated 8 weeks ago by Alex Reynolds26k

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