User: varsha619

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varsha61960
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Posts by varsha619

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Comment: C: bp overlap between multiple beds
... Thank you for your help Alex! I got the bedops and awk commands to work, as well as ended up using the 'intervene pairwise' module which gave me significance of overlap between bed files. ...
written 18 days ago by varsha61960
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Comment: C: bp overlap between multiple beds
... Thanks for the explanation Alex, I understand the method now. I have 3 files A.bed B.bed C.bed and when I do the last step - bedmap --count --bases-uniq --delim '\t' partition.bed union.bed The resulting file had values of 4 and 5 in column 1, which from your explanation is the number of fil ...
written 29 days ago by varsha61960
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Comment: C: bp overlap between multiple beds
... Hi Alex, I am a little confused with the output of bedmap. Is the 1st column number of overlaps and 2nd column bp overlap? 2 153 1 70 2 88 Is there a way to also see which files have these overlaps? Thank you!! ...
written 29 days ago by varsha61960
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bp overlap between multiple beds
... Hello, I was wondering what would be the best tool to identify and plot a venn of number of bp overlap between more than 3 bed files (similar to bedtools intersect -wo for 2 files). I have read all the related threads on multiInter and bedops. I also tried Homer mergePeaks --venn option and I ...
bedtools venn multiinter written 4 weeks ago by varsha61960 • updated 4 weeks ago by Alex Reynolds22k
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Comment: C: Finding An Genomic Intervals Shared For A Given Individual As Called By Two Or M
... Hello, this works great to compare multiple bed files. Though I was wondering if there is an option in multiIntersectBed to output the number of bp overlap between multiple bed files (similar to bedtools intersect -wao option). Please let me know, thank you! ...
written 4 weeks ago by varsha61960
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Comment: C: wig files to bigwig using UCSC kent
... Thank you for the explanation, that makes a lot of sense. I am still trying to figure out the genome build of the files so I can convert them to the new build, instead of deleting the corresponding lines from the files. ...
written 4 weeks ago by varsha61960
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Comment: C: wig files to bigwig using UCSC kent
... I will get on that, thank you again for your help! ...
written 5 weeks ago by varsha61960
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Comment: C: wig files to bigwig using UCSC kent
... Hello @kennethcondon2007, thank you I will try that. Would you happen to know the reason for this issue with wigs? ...
written 5 weeks ago by varsha61960
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Comment: C: wig files to bigwig using UCSC kent
... Hello @genecats.ucsc, I was able to grep out the chrom values that did not match the chrom.sizes file using - grep -vE '(track|chr2CEN|chr3CEN|...|chrU)' Now when I run wigToBigWig, I get the error - Overlap on chr3. Please remove overlaps and try again. This makes me worry a little since I am no ...
written 5 weeks ago by varsha61960
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Comment: C: wig files to bigwig using UCSC kent
... Hi Chris, I am not sure if that is the issue in my case. This is how my wig file format looks - 0 track type=wiggle_0 variableStep chrom=chr2L I removed the 1st line and track line before running wigToBigWig and I used fetchChromSizes to get the chrom.sizes file. Am I missing something here? Tha ...
written 5 weeks ago by varsha61960

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Popular Question 8 months ago, created a question with more than 1,000 views. For How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files

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