User: tamadomi

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tamadomi10
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3 years, 8 months ago
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Posts by tamadomi

<prev • 5 results • page 1 of 1 • next >
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How to plot motif footprint?
... I want to create a footprint plot for one of the motifs that I have identified in my data, I know the X axis should be centered at the motif center and +/- 75 bp; and the Y axis should be the number of cleavage events. I have Bam, bed and the motifs files for my data, but I'm unsure on how to cente ...
footprint homer motif plot written 3.7 years ago by tamadomi10
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Comment: C: Error when uploading Wig file to USCS
... Apologies, I meant UCSC ...
written 3.7 years ago by tamadomi10
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Error when uploading Wig file to UCSC
... I used this script (found in the forum) to convert a sorted BAM with uniquely mapped reads to wig format: samtools mpileup -BQ0 run.sorted.bam | perl -pe '($c, $start, undef, $depth) = split;if ($c ne $lastC || $start != $lastStart+1) {print "fixedStep chrom=$c start=$start step=1 span=1\n";}$_ ...
wig upload uscs written 3.7 years ago by tamadomi10
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Further analysis after motif finding?
... I have been trying yo analyse the results from the motif analysis I performed with Homer, comparing the motifs in my 2 treatments and finding information about the top motifs. I was wondering what further analysis can be performed after this? ...
motif analysis written 3.7 years ago by tamadomi10
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Motifs: de novo vs known, number of hits
... Hi! I'm analysing ATAC-seq data from cancer tissue and normal tissue. I am now analysing the results from Homer after doing the motif finding step. My supervisor has put special interest (if not all) in the "de novo" motifs found. If I understand correctly, these are unknown motifs that are matche ...
de novo homer motif written 3.7 years ago by tamadomi10

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