User: Joseph Pearson

gravatar for Joseph Pearson
Reputation:
410
Status:
Trusted
Location:
UNC Chapel Hill
Last seen:
3 years, 5 months ago
Joined:
3 years, 7 months ago
Email:
j***********@gmail.com

Posts by Joseph Pearson

<prev • 66 results • page 1 of 7 • next >
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Comment: C: How to Collapse Bedtools reciprocal overlap regions
... My mistake, I made a syntax error and a logic error. "$3==startB" needs to be "$3==endA". Sorry about that. It seemed to work for me, where I get three lines as output: chr1    353     6405    chr1    353     6447 chr1    355     6389    chr1    353     6447 chr1    501     6401    chr1    353     ...
written 3.5 years ago by Joseph Pearson410
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Comment: C: How to Collapse Bedtools reciprocal overlap regions
... Sorry, didn't make that clear. "boogens.txt" would be your output from intersectBed, like you had as the second output file in your initial question, which has six columns:columns 1-3 are a peak from file 1 (possibly repeated over multiple lines, if multiple matches in file 2), and columns 4-6 are t ...
written 3.5 years ago by Joseph Pearson410
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Answer: A: How to Collapse Bedtools reciprocal overlap regions
... I think awk would be a good approach to this, as it is great for processing columnar data. I'm not on a computer with awk at the moment, so I can't verify that the syntax will be perfect, but... awk 'BEGIN{OFS="\t"};{if ($1==chrA && $2==startA && $3==endA){endB=$6} else {print chrA,s ...
written 3.5 years ago by Joseph Pearson410
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Comment: C: Bedtools Intersect Error
... Weird, wonder if it has something to do with the size of the interval. Anyway, yeah, an awk one-liner or excel formula should be able to fix that. Sure is frustrating, though! ...
written 3.5 years ago by Joseph Pearson410
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Comment: C: Bedtools Intersect Error
... I'm not sure why that's happening, but as long as the coordinates are correct (except that they are reverse order), you can fix this with awk (or excel). Do the ranges look right? ...
written 3.5 years ago by Joseph Pearson410
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Answer: A: Bedtools Intersect Error
... The end site is before the start site. ...
written 3.5 years ago by Joseph Pearson410
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Comment: C: How to get only rows with values in at least 3 columns?
... There are four data columns, so less-than-three could be two, which means that only two have non-zero values. I'm assuming (and you did too in your for loop) that OP didn't mean to count the label column as a non-zero. ...
written 3.5 years ago by Joseph Pearson410
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Comment: C: How to get only rows with values in at least 3 columns?
... Nice go at a one-liner solution, but I think this will give a different answer, it will print if fewer than three of the replicates have a '0' value. To find only rows with at least three replicates that are non-zero, this awk command should work: awk 'BEGIN{FS="\t";OFS="\t"};{count=0;for(i=2; i&l ...
written 3.5 years ago by Joseph Pearson410
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Answer: A: GFF and Genome Fasta file
... Yes, the chromosome names must be exact matches (unless things have changed recently), so having "ChrX" vs "X" in different files will be an issue. The *nix command-line utility "sed" would be the best option, and it would be simpler (fewer changes) to change the fasta file chromosome names to matc ...
written 3.5 years ago by Joseph Pearson410
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Comment: C: cufflinks splicing analysis drosophila - 'notest' in output
... Fantastic news, glad to help. ...
written 3.5 years ago by Joseph Pearson410

Latest awards to Joseph Pearson

Supporter 3.5 years ago, voted at least 25 times.
Rising Star 3.5 years ago, created 50 posts within first three months of joining.
Scholar 3.5 years ago, created an answer that has been accepted. For A: bedtools 2.25 vs bedtools2.20 coverageBed output not consistent
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Intersecting ChIP/RNA-seq data
Scholar 3.5 years ago, created an answer that has been accepted. For A: bedtools 2.25 vs bedtools2.20 coverageBed output not consistent
Scholar 3.5 years ago, created an answer that has been accepted. For A: bedtools 2.25 vs bedtools2.20 coverageBed output not consistent
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Intersecting ChIP/RNA-seq data
Scholar 3.6 years ago, created an answer that has been accepted. For A: bedtools 2.25 vs bedtools2.20 coverageBed output not consistent

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