How to plot the Saturation curves to assess the sequencing depth?

[Brian Bushnell]

Thanks very much Brian.

I downloaded BBMap and when I tried to run (bbcountunique.ssh) I got the following error "Exception in thread main java.lang.unsupportedclassversionerror: jgi/Calcuniqueness"

I downloaded a new version of jre but I am wondering how to use it with the code? do I need to modify the code or the path variable? do I need to download another file?

Assuming you downloaded a Java 7 JRE, and installed it, the program should just work. If you are still getting the same error, then the JRE was not installed correctly; you can resolve that by editing your PATH variable to remove the path to the old java executable (on our system, it is "/usr/common/usg/languages/java/jdk/oracle/1.7.0_51_x86_64/bin/") and put in the path to the new java executable. Alternately, you can edit the shellscript "bbcountunique.sh". Line 80, 5 lines from the bottom, is:

local CMD="java $EA $z -cp $CP jgi.CalcUniqueness $@"

If your new java executable is at, say, "/usr/jdk/oracle/1.7.0_51_x86_64/bin/java", then you would just change that line to:

local CMD="/usr/jdk/oracle/1.7.0_51_x86_64/bin/java $EA $z -cp $CP jgi.CalcUniqueness $@"

If you can't figure out how to install the new jre or don't have the proper permissions, then run "java -version" and copy and paste the output into this thread.

[Fernas]

Thanks very much Brian.

I downloaded BBMap and when I tried to run (bbcountunique.ssh) I got the following error "Exception in thread main java.lang.unsupportedclassversionerror: jgi/Calcuniqueness"

I downloaded a new version of jre but I am wondering how to use it with the code? do I need to modify the code or the path variable? do I need to download another file?

[Brian Bushnell]

Thanks Brian ! Once more!

You're welcome

[luc]

Thanks Brian ! Once more!

[Brian Bushnell]

I have a program for plotting library uniqueness as you go through the reads. The graphs look like this:


It works by pulling kmers from each input read, and testing whether it has been seen before, then storing it in a table.

The bottom line, "first", tracks whether the first kmer of the read has been seen before (independent of whether it is read 1 or read 2).

The top line, "pair", indicates whether a combined kmer from both read 1 and read 2 has been seen before. The other lines are generally safe to ignore but they track other things, like read1- or read2-specific data, and random kmers versus the first kmer.

It plots a point every X reads (configurable, default 25000).

In noncumulative mode (default), a point indicates "for the last X reads, this percentage had never been seen before". In this mode, once the line hits zero, sequencing more is not useful.

In cumulative mode, a point indicates "for all reads, this percentage had never been seen before", but still only one point is plotted per X reads.

Sample command line:

bbcountunique.sh in=reads.fq out=histogram.txt

Note that the lines are not perfectly smooth; the little peaks are caused by high-error tiles. But it's still useful in that it allows assessment of a library that lacks a reference.

[Fernas]

Dear all,

I want to know if there is a tool or ready-script that I can use to plot the Saturation (Rarefaction) plot in order to assess the sequencing depth of the sequenced libraries that I have.