Hi Roni,
These are exposed as public APIs. If you want, you can run them inside of the
adam-shell (which is just a wrapper for the spark shell, but with the ADAM
libraries on the class path).
Also , I need to save all my intermediate data. Seems like ADAM stores data
in Parquet on HDFS.
I
Hi Frank,
Thanks for the reply. I downloaded ADAM and built it but it does not seem
to list this function for command line options.
Are these exposed as public API and I can call it from code ?
Also , I need to save all my intermediate data. Seems like ADAM stores
data in Parquet on HDFS.
I want
Sorry for the delay.
The files (called .bed files) have format like -
Chromosome start endfeature score strand
chr1 713776 714375 peak.1 599+
chr1 752401 753000 peak.2 599+
The mandatory fields are
1. chrom - The name of the chromosome (e.g. chr3, chrY,
Hi Roni,
We have a full suite of genomic feature parsers that can read BED, narrowPeak,
GATK interval lists, and GTF/GFF into Spark RDDs in ADAM Additionally, we have
support for efficient overlap joins (query 3 in your email below). You can load
the genomic features with
I want to use spark for reading compressed .bed file for reading gene
sequencing alignments data.
I want to store bed file data in db and then use external gene expression
data to find overlaps etc, which database is best for it ?
Thanks
-Roni
Can you describe your use case in a bit more detail since not all people on
this mailing list are familiar with gene sequencing alignments data ?
Thanks
On Fri, Jun 5, 2015 at 11:42 PM, roni roni.epi...@gmail.com wrote:
I want to use spark for reading compressed .bed file for reading gene
