PublicDatasetsNgs

= Public Genomes and indexes for NGS =

cheaha:/lustre/project/public_datasets/ngs

CCTS BMI in conjunection with anyone who wishes to participate, maintains a public directory of genomic sequences and indexes built from them for use with a variety of NGS alignment and analysis programs, for use both from the command-line and within the Galaxy environment

See also NgsCcts for programs that build and use these indices and databases.

WARNING: these datasets are currently under construction. Contact curtish A uab.edu with questions.

= Directory Structure = * curator: ngs-ccts group
 * GIT:/??/scripts
 * /lustre/project/public_dataset/ngs

Notes on what CCTS BMI wants to populate
rsync --list-only --dirs -lptgoDzvP datacache.g2.bx.psu.edu::indexes rsync --list-only --dirs -lptgoDzvP datacache.g2.bx.psu.edu::indexes/microbes/ rsync --list-only --dirs -lptgoDzvP datacache.g2.bx.psu.edu::location
 * Order chroms
 * Galaxy Rsync
 * see http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
 * 1) list available dbkeys
 * 1) list available dbkeys for "microbes"
 * 1) list available .loc files

rsync --list-only -azvP rsync://datacache.g2.bx.psu.edu/indexes/mm9 /lustre/project/public_datasets/ngs/galaxy-datacache/indexes rsync -azvP rsync://datacache.g2.bx.psu.edu/indexes/mm9 /lustre/project/public_datasets/ngs/galaxy-datacache/indexes rsync --exclude align/ -azvP rsync://datacache.g2.bx.psu.edu/indexes/mm9 /lustre/project/public_datasets/ngs/galaxy-datacache/indexes rsync -azvP rsync://datacache.g2.bx.psu.edu/location/ /lustre/project/public_datasets/ngs/galaxy-datacache/location/
 * 1) list mm9 dir/file tree
 * 1) pull down mm9 (all)
 * 1) pull down mm9 w/o alignment files
 * 1) pull down all loc files


 * UCSC
 * Hg19 – chromFa.tar.gz
 * Mm9, Mm10
 * Rn4, Rn5
 * Zv9=DanRer7
 * Ensembl (need chr); gtf + fasta
 * TreeShrew (don’t add chr!)
 * SacSer2, SacSer3 (so it will match SNPeff – ignore SM/RM – alphabetic order
 * GHR37
 * Celegans (rel66) WS220.release66 (ce10.66)
 * NCBI
 * VacvWR
 * Mycoplasm Genomes
 * HCMV

GATK – resource bundle.
 * why UCSC ?
 * Download all chrom, including UNKNOWN chroms
 * unknown chroms missing from Illumina
 * Ensemble missing “chr” prefix
 * GATK Chrome order
 * "new" GATK order
 * [dkcrossm] For humans, if you use UCSC's genome, then mitochondria goes first, then numerically (chrMt, chr1, chr2...chrX, chrY). If you use another human genome (from 1000 genome project), then it goes in numerical order with mitochondria after the chrY (chr1, chr2, chr3...chrY, chrMt).
 * For non-humans, it doesn’t seem to matter. I've tried it both ways.  In a C. elegans study, I had mitochondria first.  In a yeast study, I had mitochondria last, and they both worked.  So, I guess non-humans chromosome order isn't critical.
 * [dkcrossm] It seems that GATK has reversed their policy again on the chromosome order for humans (it doesn’t say anything about the other species chromosome orders, so that is still left up in the air). I’ve copied their section on human chromosome order for your reference:
 * If you are using human data, your reads must be aligned to one of the official b3x (e.g. b36, b37) or hg1x (e.g. hg18, hg19) references. The contig ordering in the reference you used must exactly match that of one of the official references canonical orderings. These are defined by historical karotyping of largest to smallest chromosomes, followed by the X, Y, and MT. The order is thus 1, 2, 3, ..., 10, 11, 12, ... 20, 21, 22, X, Y, MT. The GATK will detect misordered contigs (for example, lexicographically sorted) and throw an error. This draconian approach, though unnecessary technically, ensures that all supplementary data provided with the GATK works correctly. You can use ReorderSam to fix a BAM file aligned to a missorted reference sequence.
 * old Order GATK Human
 * Mitochondria, 1…26, X, Y, Unknown by chrom + num order
 * BWA .62 version
 * Bowtie 2 (though not in galaxy)
 * SNPeff2.1 SNPeff3.0 download tools
 * Galaxy rsync
 * dbSNP
 * 1000genome
 * Mils
 * GTF downloads
 * Bedtools gff3 -> gtf
 * Embl needs chr
 * UCSC needs gtf + refgene then my script to get good GTF

galaxy data-cache

 * Galaxy docs on builds.txt search docs
 * .2bit to .fa conversion for datacache and
 * directory structure
 * XXX = {mm9, hg19, etc}
 * bowtie_index/XXX.*
 * cs/XXX.*
 * bwa_index/XXX.*
 * chrom/chr*.fa
 * download/(date)/md5sum*
 * liftover/XXXToYYY.over.chain
 * picard_index/XXX.{dict,.fai}
 * sam_index/XXX.fai (identical to .fai in picard_index!)
 * seq/XXX.2bit