User: kerrypop

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kerrypop0
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Posts by kerrypop

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Comment: C: Bedtools intersect returns 0, intersections present on IGV
... That did it - thank you! ...
written 3 days ago by kerrypop0
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Comment: C: Bedtools intersect returns 0, intersections present on IGV
... I only used chromosome coordinates but don't see any extraneous characters cat -vet gene.ROI | head Chr6^I11711888^I11781280$ Chr6^I35702809^I35718690$ Chr1^I162349520^I162358608$ ...
written 3 days ago by kerrypop0 • updated 3 days ago by Pierre Lindenbaum102k
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Comment: C: Bedtools intersect returns 0, intersections present on IGV
... Yes, same chromosome notation. Files are not sorted - I've done this analysis before and didn't sort them. Do you think sorting would overcome this? The ROI file is just a document, created using nano in terminal. The other is a broad peak file. ...
written 3 days ago by kerrypop0
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Comment: C: Bedtools intersect returns 0, intersections present on IGV
... Here's zoomed in screenshot of the first ROI. There should be 4 intersections. https://imgur.com/a/lsiEQ ...
written 3 days ago by kerrypop0
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Bedtools intersect returns 0, intersections present on IGV
... Hello, I am trying to use bedtools to find intersections between H3K4me1 peaks and my regions of interest. Though I can see overlap on IGV, intersect returns 0 without any error messages. Here is command I'm using and screenshot from IGV: bedtools intersect -a gene.ROI -b wgEncodeBroadHiston ...
bedtools chip-seq written 4 days ago by kerrypop0

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