hurwitzlab/mg-sample-data

Name: mg-sample-data

Owner: Hurwitz Lab

Description: Sample data for a metagenomic / metatranscriptomic workflow

Created: 2017-08-29 22:37:33.0

Updated: 2017-09-05 22:57:15.0

Pushed: 2018-01-03 18:32:42.0

Homepage: null

Size: 25200

Language: Shell

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README

mg-sample-data

Sample data for a metagenomic / metatranscriptomic workflow.

The dna / rna is mouse cecal matter that contains mouse, mouse chow and microbial nucleotide sequences.

Full data is here.

Centrifuge database of bacteria available here – ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz

CAUTION: ~5GB file.

explanation of directories / files

• /dna

  Two samples of 2500 paired (R1,R2) 100bp reads (cancer and control).

• /rna

  Two samples of 2500 paired (R1,R2) 100bp reads (matched to dna).

• /annotation

  Annotation from Patric in tab-delimited and gff formats.

• /genomes

  Two bacterial reference genomes from Patric.

• /metadata

  Metadata of genomes including their taxonomic lineage.

• /scripts

  Sample scripts to run on PBS scheduling system.

• /scripts/workers

  “Worker” scripts that are launched by the jobs running on the HPC/HTC. Can be modified to run interactively if needed.