| fetchChromSizes |
fetchChromSizes <db> > <db>.chrom.sizes |
Fetch chrom.sizes information from UCSC for the given <db> |
| vdb-decrypt |
vdb-decrypt [options] <source-file> <destination-file> |
Decrypt non-SRA dbGaP data ("phenotype data") |
| bedToExons |
bedToExons originalBeds.bed splitBeds.bed |
Split a bed up into individual beds (one for each internal exon). |
| prefetch |
prefetch [options] <SRA accession> |
Download SRA, dbGaP, and ADSP data from NCBI |
| hgWiggle |
hgWiggle [options] <track names ...> |
Fetch wiggle data from UCSC Genome Browser's database or a wig file |
| fastq-dump |
fastq-dump [options] <path/file> [<path/file> ...] |
This tool extracts reads from SRA archives. |
| vdb-encrypt |
vdb-encrypt [options] <source-file> <destination-file> |
Encrypt non-SRA dbGaP data ("phenotype data") |
| abi-dump |
abi-dump [options] <accession> |
Convert SRA data into ABI format (csfasta / qual) |
| vdb-encrypt |
vdb-encrypt [options] <directory> |
Encrypt non-SRA dbGaP data ("phenotype data") |
| sra-stat |
sra-stat [options] <path/file> [<path/file> ...] |
Generate statistics about SRA data (quality distribution, etc.) |
| vdb-encrypt |
vdb-encrypt [options] <source-file> <destination-directory> |
Encrypt non-SRA dbGaP data ("phenotype data") |
| vdb-dump |
vdb-dump [options] <path/file> [<path/file> ...] |
Output the native VDB format of SRA data. |
| vdb-dump |
vdb-dump [options] <accession> |
Output the native VDB format of SRA data. |
| vdb-encrypt |
vdb-encrypt [options] <source-file> |
Encrypt non-SRA dbGaP data ("phenotype data") |
| sra-stat |
sra-stat [options] <accession> |
Generate statistics about SRA data (quality distribution, etc.) |
| fasterq-dump |
fasterq-dump <accession> [options] |
Extract data in FASTQ- or FASTA-format from SRA-accessions |