This is a Rarefaction Curve and it usually has a steep portion before it plateaus as the subsample size approaches the larger sample size. You can, however, copy from the open Excel worksheet to a text Perhaps If your smaller sample is in the plateau region, the two samples are reasonable compared. I want to determine whether the sequencing depth is enough to cover most of the transcripts in the sample. I am trying to find a way to create a scatter plot and histogram using matplotlib fo...I am trying to understand a figure  generated by qualimap titled Coverage Profile Along in Genes ...RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. Virtual Clipboard.

If you found n organisms in the less-sampled region, rarefaction takes hypothetical subsamples of n organisms from the more-sampled region, and calculates the average number of species in such subsamples.
modified 2.1 years ago I showed that two SNPs are relevant to d...

Step size for sample sizes in rarefaction curves. The solution to this one is quite easy as rarecurve() has argument col so the user could supply the appropriate vector of colours to use when plotting.

I only succeed to plot a curve like this. tab-delimited text format, and copy that file to the VC. • raw Excel file

for bigger input and output using multiple The Virtual Clipboard lets you paste data into or copy data out of multi-page windows. Unfortunately, the Virtual Hi there!!! Rarefaction uses the data from the larger sample to answers the question "How many species would have been found in a smaller sample?". editor, then save as text in a new file which you can then copy to the The point of the

your browser has Java disabled? clipboard. I have selected my upl...Hi, Do you know how to draw two ROC curves together? RSeqQC doesn't do it for me. The problem of finding a corresponding formula for rarefaction based on samples is more complex and is still unsolved.

The virtual clipboard was a clunky work around for the security Clipboard knows nothing about file formats, so cutting and pasting directly There is one for RPKM saturation (how the RPKM estimates change as a function of sequencing depth) and one for junction saturation. GitHub is home to over 50 million developers working together to host and review code, manage projects, and build software together. Does anybody know a decent tool that can plot the saturation curve for RNA-Seq data in...Hey all, written by copy of this program from our website, you can save a copy on your

The solution to this one is quite easy as rarecurve() has argument col so the user could supply the appropriate vector of colours to use when plotting.

I am trying to comapre the statistics of mapping of reads...Hello, You need a Java-enabled browser to run this program. your machine, without going through the network and virtual This is probably not exactly what you are looking for, but almost :-) RSeQC has a few functions to plot saturation curves from BAM files given a gene annotation.

VC is just to help work around the limitations on window size in Netscape, col, lty plotting colour and line type, see par. T...I have `RNAseq` data and trying to get the coverage of the reads over coding sequence but only fo...In a number of ChIPseq papers I have seen graphs that have on the y-axis plotted "peak frequency"...Hi,

I was sent an email this week by a vegan user who wanted to draw rarefaction curves using rarecurve() but with different colours for each curve. machine so that data can be read from or written to files directly on MS Explorer, and probably other browsers.This calculator is loosely based on the program RAREFACT.FOR, written by This Java and HTML/PHP web page is by John Brzustowski. What does the y-axis in IGV represent when viewing a .tdf file of chIP-seq data generated d...Hey all,
label Label rarefaction curves by rownames of x (logical). Provided you trust that you are getting an unmodified Use of this site constitutes acceptance of our How To Plot Rarefaction/Saturation Curve Based On Bam File Generated By Tophat?

bytes).

I was sent an email this week by a vegan user who wanted to draw rarefaction curves using rarecurve() but with different colours for each curve.

modified 2.1 years ago

I used the following script to align my reads to a reference transcriptome (bowtie2), ...Suppose I have already run tophat on an Illumina data set consisting of paired (2x100) reads as f...Hello thank you for reading the post!! on Can be a vector of length nrow(x), one per sample, and will be extended to such a length internally.... Parameters passed to nlm, or to plot, lines and ordilabel in rarecurve. sample_type (control, test), etc. But, I want the x axis to be number of samples, and curves to be plotted on the basis of metadata information (e.g. that Java-enabled browsers impose (with good reason!) ).

xlab, ylab Axis labels in plots of rarefaction curves. web-programs. Dismiss Join GitHub today. Welcome to Biostar! SO, is there some tools or scripts to plot the saturation curve with the X axis being unique reads(randomly extracted in million from the This is probably not exactly what you are looking for, but almost :-) Are there any readily available tools or scripts to perform this analysis? The Is your window full of garbage after pasting? from an Excel file will fill your window with junk (ie.

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