Merge paired-end sequences

[castrovr]

Hello

I'm new and I wonder if somebody knows is the program fastq-join requires perfect matches to merged the reads.
Maybe is obvious but I need to be sure of this information.

Thank you

[Brian Bushnell]

No, it does not. However, I've found that fastq-join does not give very good results in my tests, compared to other programs such as BBMerge (which I wrote) and Usearch.

[castrovr]

Brian

Thank you for your quick reply. I will try BBMerge and Usearch with my sequences and compare the results.

Ruth

[castrovr]

BBmerge stats.sh

Hello
I download and installed BBmap, and I tried to test the stat.sh of BBmerge but I had an error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
at java.security.SecureClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.access$100(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClassInternal(Unknown Source)
Full Command:/local/cluster/spatafora/bin/bbmap/stats.sh in=/local/cluster/spatafora/bin/bbmap/resources/phix174_ill.ref.fa.gz

What's this error means?

[GenoMax]

Hello
I download and installed BBmap, and I tried to test the stat.sh of BBmerge but I had an error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
at java.security.SecureClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.access$100(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClassInternal(Unknown Source)
Full Command:/local/cluster/spatafora/bin/bbmap/stats.sh in=/local/cluster/spatafora/bin/bbmap/resources/phix174_ill.ref.fa.gz

What's this error means?

Do you know which version of Java you are using? @Brian validates BBMap against Java 7/8 (not sure if 6 is supported any more).

[Brian Bushnell]

Java 6 does work for most of the programs (except BBNorm), though I don't test with it anymore. This error message looks like it's from Java 5 or earlier. Please try running this, on the command line:

java -Xmx100m -version

[castrovr]

Yes, it seems I was using an older version of Java, I change that and run the test and it works!. Now I running my own data. No error messages yet.
Thank you

[castrovr]

Create a short insert library in silico

Hello all,

I have I genome assembly that I made with velvet, and now I want to create in silico a short insert library of ~250pb. Which program in your experience is better to do this?

Thanks

[Brian Bushnell]

I'd suggest RandomReads. You can use it like this:

(index the reference)
bbmap.sh ref=assembly.fa

(generate reads)
randomreads.sh out=reads.fq.gz reads=5m paired len=100 mininsert=150 maxinsert=350 bell adderrors

That will get a 250bp insert average, with a bell-shaped distribution, and 100bp reads. The file will be interleaved but you can get reads in 2 files with the out1 and out2 flags if you want.

[castrovr]

Thank you Brian