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Available software:
This collection is always growing. To view what is actually there, do the following:
> ls /cluster/tufts/ngsp/ngsp/bin | more
Use the space bar to page the listing.
Bowtie indices and annotations from Illumina for the Mouse
Illumina annotation and index information can be found in:
/cluster/tufts/ngsp/ngsp/Mus_musculus/Ensembl
/cluster/tufts/ngsp/ngsp/Mus_musculus/UCSC
For ENSEMBL:
The annotations is at:
/cluster/tufts/ngsp/ngsp/Mus_musculus/Ensembl/NCBIM37/Annotation/Archives/archive-2013-03-06-18-55-12/Genes/genes.gtf
and the bowtie indices are in:
/cluster/tufts/ngsp/ngsp/Mus_musculus/Ensembl/NCBIM37/Sequence/BowtieIndex
For UCSC: The corresponding files are in directories named Sequence and Annotation
Remember: UCSC used "chr" but ENSEMBL uses on number to name chromosomes.
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end) Bowtie documentation
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