User: Lucy

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Lucy0
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Posts by Lucy

<prev • 22 results • page 1 of 3 • next >
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Homer annotatePeaks.pl custom GTF
... Hi, I am running Homer annotatePeaks.pl to assign my ATAC-seq peaks to genes. For the annotation, I am using a custom Ensembl GTF file and a custom Ensembl TSS file. annotatePeaks.pl peaks.txt hg38 -gtf Ensembl_hg38.gtf -cTSS Ensembl_hg38.tss > annotated_peaks.txt When using a custom GTF ...
gtf homer atac-seq written 7 weeks ago by Lucy0
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Comment: C: Aligning RNA-seq and ATAC-seq gene annotations
... Only 26465/66908 peaks have Ensembl IDs that match those in the RNA-seq data. However, when I used the default Homer annotation, 40709/66908 peaks had Ensembl IDs that match those in the RNA-seq file. There are still problems with the default annotation though. For example in some cases, genes wi ...
written 9 weeks ago by Lucy0
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Aligning RNA-seq and ATAC-seq gene annotations
... Hi, I have matched RNA-seq and ATAC-seq data from two cell subsets and I am trying to compare the expressed genes from the RNA-seq data with the accessible peaks from the ATAC-seq data. However, I have found that the methods which I used to annotate the expressed genes and accessible peaks use dif ...
homer gene annotation atac-seq rna-seq written 9 weeks ago by Lucy0
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Comment: C: FRIP score ATAC-seq
... Great thank you - this worked well. ...
written 10 weeks ago by Lucy0
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Comment: A: HOMER de novo motif enrichment
... Thank you - yes I have read this. Based on this, I thought the hypergeometric sounded appropriate. With binomial scoring, Homer identified 27 enriched motifs, compared to 3 using hypergeometric. The reason that I am unsure of the best approach is that elsewhere in the Homer documentation, it says ...
written 3 months ago by Lucy0
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HOMER de novo motif enrichment
... Hi all, I am performing Homer findMotifsGenome.pl to identify motifs enriched in a subset of ATAC-seq peaks (~2500 peaks) vs. a control set of ATAC-seq peaks (~4000 peaks). I ran the command using either the binomial distribution to score motifs or hypergeometric enrichment scoring. Changing th ...
homer motif enrichment written 3 months ago by Lucy0
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ATAC-seq transcription factor binding prediction
... Hi, I am trying to predict transcription factor binding sites from ATAC-seq data, for which I also have matched RNA-seq. I have read a lot of papers recently suggesting different methods for doing this (all of which claim that they are better than the other techniques). I was wondering whether an ...
transcription factor atac-seq rna-seq written 4 months ago by Lucy0 • updated 5 weeks ago by am26220
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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 4 months 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 4 months ago by Lucy0 • updated 3 months ago by Biostar ♦♦ 20
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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 months ago by Lucy0 • updated 5 months ago by genomax63k

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