User: gtasource
gtasource • 10
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Posts by gtasource
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... I have the following bed file
chr1 18551 18579
chr1 18559 18583
chr1 18966 18991
chr1 18966 18991
chr1 18966 18993
I want to expand the coordinates to generate a new file that lists every single coordinate individually. For example:
chr1 18551 18552
chr1 18552 18 ...
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Comment:
C: edgeR RPKM Values
... After the RPKM step, I receive this errror:
Warning message:
In Ops.factor(left, right) : ‘/’ not meaningful for factors ...
written 11 weeks ago by
gtasource • 10
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... Hello,
I am trying to use edgeR to calculate RPKM values. However, when I have searched for help on this topic. I've still not been able to make sense of the existing R codes to work for me. Here's my current code:
data_raw <- read.table("counts.txt", header = TRUE)
group <- c(rep( ...
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... Using Bedtools makewindows, I generated a file that split up the genome by 5000kilobase windows. Using Bedtools Coverage, I then found how many reads fell into these 5000kb windows from a specific BAM file. Now that I am looking at the Bedtools Coverage results, I see that the following pieces of ...
written 3 months ago by
gtasource • 10
• updated
3 months ago by
Kevin Blighe ♦ 21k
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... Hello,
I am looking to find the difference in read depth between two bam files (A, B.) My initial idea was to use Bedtools, find the total coverage of A and B, and then use Bedtools intersect to compare where they overlap and do not. However, I'm just curious if anybody has alternative suggestion ...
written 6 months ago by
gtasource • 10
• updated
6 months ago by
Pierre Lindenbaum ♦ 108k
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... Removed this postRemoved this postRemoved this postRemoved this postRemoved this postRemoved this postRemoved this postRemoved this postRemoved this post ...
written 18 months ago by
gtasource • 10
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