Beginner's Guide to Data Import

This guide describes how to import instrument data into GMS using the downsampled TST1 dataset (TST1ds) as an example. You can follow these steps to import TST1ds yourself. Before continuing you must have already run the ./setup/prime-system.pl command as documented in the installation instructions.

Instead of completing the following steps by hand, you may choose to run the already scripted version of these steps here: ./downsampled-demo-data/example-import-data.sh. Or you may choose to follow the instructions in the rest of this guide, which describes the commands executed by example-import-data.sh. Even if you choose not to execute example-import-data.sh as-is, it provides a complete example of importing data into GMS.

In order to import an instrument data file, there must exist a record in GMS of the library which was sequenced, the sample from which the library was derived, and the individual from which the sample was collected. So, in order to import a set of instrument data files, an individual, one or more samples, and one or more libraries must first exist or be created in GMS.

Setup the Individual

genome individual create                                                        \
    --name="H_NJ-HCC1395ds"                                                     \
    --upn='HCC1395ds'                                                           \
    --common-name="TST1ds"                                                      \
    --gender=female                                                             \
    --taxon="name=human"

The value of the --name argument is arbitrary, but it should be something representative of the individual because you'll reference this name later when adding samples for this individual to GMS.

Setup the Samples

genome sample create                                                            \
  --name='H_NJ-HCC1395-HCC1395_BL_RNAds'                                        \
  --source="name=H_NJ-HCC1395ds"                                                \
  --common-name='normal'                                                        \
  --tissue-desc='b lymphoblast'                                                 \
  --extraction-type='rna'                                                       \
  --extraction-label='HCC1395 BL_RNA'                                           \
  --cell-type='primary'

The --source parameter references the individual created in the previous step. Notice how the value of the --source parameter here matches the --name parameter given to genome individual create.

The argument to the --extraction-type parameter can be either rna or genomic dna.

Repeat the genome sample create command for each sample in your dataset. The TST1ds dataset has four samples.

Setup the Libraries

genome library create                                                           \
  --name="Pooled_RNA_2891006726-mR1-cD1-lg1-lib1ds"                             \
  --sample="H_NJ-HCC1395-HCC1395_BL_RNAds"                                      \
  --protocol='Illumina Library Construction'                                    \
  --original-insert-size='364'                                                  \
  --library-insert-size='483'                                                   \
  --transcript-strand='unstranded'

The genome library create command creates a record of a library in GMS. The library links to the sample from which it was created, so it is important that the argument to --sample here matches the argument to --name given to the genome sample create command above, to indicate which sample record in GMS this library record should link to.

The --transcript-strand parameter is specified because the extraction-type of this library's sample is rna. The --transcript-strand parameter accepts one of three values as its argument. Possible values are 'unstranded', 'firststrand', or 'secondstrand'. This parameter should not be used for samples with extraction type genomic dna.

If your library is a capture library, create it just as you would a library for genomic dna. When you import the instrument data, you will have the opportunity to specify a capture set during import.

Import the Instrument Data

genome instrument-data import basic                                             \
    --import-source-name='GMS'                                                  \
    --instrument-data-properties='read_length=100,clusters=170049877'           \
    --source-files="gerald_C2DBEACXX_3.bam"                                     \
    --library="Pooled_RNA_2891006726-mR1-cD1-lg1-lib1ds"

The genome instrument-data import basic command imports sequence reads. This step depends on already having a library created, as in the previous step, and it requires the argument to --library match the argument to --name given to genome library create. This step imports reads from a bam file, which in this example, exists in a file named gerald_C2DBEACXX_3.bam in the current working directory.

Defining Models and Running Builds

To make use of the instrument data, genome models must be defined which use the instrument data, and builds must be executed for those models. Once data has been imported, the genome clin-seq advise --allow-imported --individual='TST1ds' command can be used to guide you through the process of defining models and running builds on those models.

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