Target enrichment performance

[bpetersen]

Thanks for the quick reply!
I am using the following syntax:
java NGSrich -r /path/to/file.sam -a hg18 -T /path/to/temp_folder -t /path/to/sure_select_targets.bed
The sam file was generated with bwa and I am in the bin folder of NGSrich.
Regards,
BP

[pfrommolt]

Okay, which syntax are you using for the analysis? Is your read alignment file in SAM format?

Regards, Peter

[bpetersen]

Yes, my data are from human samples. But I get the following error:
=======================1=======================
>>> STEP 1: reducing files

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Array index out of range: 3
at java.util.Vector.get(Vector.java:721)
at adapter.Adapter.field(Adapter.java:90)
at adapter.readAdapter.SamAdapter.pos(SamAdapter.java:184)
at adapter.readAdapter.SamAdapter.adapt(SamAdapter.java:131)
at Enrichment.reduceFiles(Enrichment.java:177)
at NGSrich.main(NGSrich.java:91)

[pfrommolt]

The genome annotation parameter is not supposed to be a file. You just need to specify the UCSC version number, e.g. 'hg19' and the software will download the correct annotation from the internet. Are you using data from a human sample?

Best,
Peter

[bpetersen]

Dear Peter and Ali,
Your tool sounds great! I just have a question about its usage.
I get an error when trying it out, but this might be because I probably specified the wrong file for the parameter -a or -g. What kind of file is the "genome annotation" supposed to be and where can I get it? I specified the genome as a fasta file, but I am pretty sure that's not what is needed, right?
Can't wait to get this working, thanks for your help!

[pfrommolt]

Java version of NGSrich

Dear All,

we have now prepared a fully-functional Java version of NGSrich which allows you to do a quick and detailed performance check for your target-enriched resequencing projects. We are using this as part of an exome analysis pipeline in our medium-sized genome center.

The reports can be integrated into a webserver in a very efficient and user-friendly way. You should definitely download this and give it a try!

Best,
Peter and Ali

[pfrommolt]

Dear All,

I would like to announce the inception of NGSrich, a software for evaluation of target enrichment performance in Illumina next-generation sequencing. An early release of the code has been uploaded to SourceForge at

http://sourceforge.net/projects/ngsrich/files/

but we're still working on a Java version. Regards,

Peter Frommolt
University of Cologne