Preparing the Input Data¶
Config file¶
The config file is in YAML format. It is composed of general and module-specific parameters. In YAML, a variable can be of the following types: boolean, string, numeric, list and dictionary. They are declared by writing the variable name followed by a colon, a space, and the value, for example:
# A boolean is binary and can be true of false
boolean_var: true # or false
# A string is a text. Quotation marks are not needed.
string_var: whatever text
# A numeric can be an integer or a real number. A dot separates a decimal.
numeric_var: 0.05
# A list is a collection of elements of the same type.
list_var:
- element_1 # elements are indented
- element_2
# A dictionary contains key-value pairs. It is a collection of multiple
# elements where the key is a string and the value any type.
dictionary_var:
key_1: value_1
key_2: value_2
Now we describe the different parameters needed in DROP.
Global parameters¶
| Parameter | Type | Description | Default/Examples |
|---|---|---|---|
| projectTitle | character | Title of the project to be displayed on the rendered HTML output | Project 1 |
| htmlOutputPath | character | Full path of the folder where the HTML files are rendered | /data/project1/htmlOutput |
| indexWithFolderName | boolean | If true, the basename of the project directory will be used as prefix for the index.html file | true |
| genomeAssembly | character | Either hg19/hs37d5 or hg38/GRCh38, depending on the genome assembly used for mapping | /data/project1 |
| sampleAnnotation | character | Full path of the sample annotation table | /data/project1/sample_annotation.tsv |
| root | character | Full path of the folder where the subdirectories processed_data and processed_results will be created containing DROP’s output files. | /data/project1 |
| genome | character | Full path of a human reference genome fasta file | /path/to/hg19.fa |
| genome | dictionary | (Optional) Multiple fasta files can be specified when RNA-seq BAM files belong to different genome assemblies (eg, ncbi, ucsc). |
|
| geneAnnotation | dictionary | A key-value list of the annotation name (key) and the full path to the GTF file (value). More than one annotation file can be provided. |
|
| hpoFile | character | Full path of the file containing HPO terms. If null (default), it reads it from our webserver. Refer to Files to download. |
/path/to/hpo_file.tsv |
| tools | dictionary | A key-value list of different commands (key) and the command (value) to run them |
|
Export counts dictionary¶
| Parameter | Type | Description | Default/Examples |
|---|---|---|---|
| geneAnnotations | list | key(s) from the geneAnnotation parameter, whose counts should be exported |
- gencode34 |
| excludeGroups | list | aberrant expression and aberrant splicing groups whose counts should not be exported. If null all groups are exported. |
- group1 |
Aberrant expression dictionary¶
| Parameter | Type | Description | Default/Examples |
|---|---|---|---|
| run | boolean | If true, the module will be run. If false, it will be ignored. | true |
| groups | list | DROP groups that should be executed in this module. If not specified or null all groups are used. |
|
| minIds | numeric | A positive number indicating the minimum number of samples that a group needs in order to be analyzed. We recommend at least 50. | 1 |
| fpkmCutoff | numeric | A positive number indicating the minimum FPKM per gene that 5% of the samples should have. If a gene has less it is filtered out. | 1 # suggested by OUTRIDER |
| implementation | character | Either ‘autoencoder’, ‘pca’ or ‘peer’. Methods to remove sample covariation in OUTRIDER. | autoencoder |
| zScoreCutoff | numeric | A non-negative number. Z scores (in absolute value) greater than this cutoff are considered as outliers. | 0 |
| padjCutoff | numeric | A number between (0, 1] indicating the maximum FDR an event can have in order to be considered an outlier. | 0.05 |
| maxTestedDimensionProportion | numeric | An integer that controls the maximum value that the encoding dimension can take. Refer to Advanced options. | 3 |
Aberrant splicing dictionary¶
| Parameter | Type | Description | Default/Examples |
|---|---|---|---|
| run | boolean | If true, the module will be run. If false, it will be ignored. | true |
| groups | list | Same as in aberrant expression. | # see aberrant expression example |
| minIds | numeric | Same as in aberrant expression. | 1 |
| recount | boolean | If true, it forces samples to be recounted. | false |
| longRead | boolean | Set to true only if counting Nanopore or PacBio long reads. | false |
| keepNonStandardChrs | boolean | Set to true if non standard chromosomes are to be kept for further analysis. | true |
| filter | boolean | If false, no filter is applied. We recommend filtering. | true |
| minExpressionInOneSample | numeric | The minimal read count in at least one sample required for an intron to pass the filter. | 20 |
| minDeltaPsi | numeric | The minimal variation (in delta psi) required for an intron to pass the filter. | 0.05 |
| implementation | character | Either ‘PCA’ or ‘PCA-BB-Decoder’. Methods to remove sample covariation in FRASER. | PCA |
| deltaPsiCutoff | numeric | A non-negative number. Delta psi values greater than this cutoff are considered as outliers. | 0.3 # suggested by FRASER |
| padjCutoff | numeric | Same as in aberrant expression. | 0.1 |
| maxTestedDimensionProportion | numeric | Same as in aberrant expression. | 6 |
Mono-allelic expression dictionary¶
| Parameter | Type | Description | Default/Examples |
|---|---|---|---|
| run | boolean | If true, the module will be run. If false, it will be ignored. | true |
| groups | list | Same as in aberrant expression. | # see aberrant expression example |
| gatkIgnoreHeaderCheck | boolean | If true (recommended), it ignores the header warnings of a VCF file when performing the allelic counts | true |
| padjCutoff | numeric | Same as in aberrant expression. | 0.05 |
| allelicRatioCutoff | numeric | A number between [0.5, 1) indicating the maximum allelic ratio allele1/(allele1+allele2) for the test to be significant. | 0.8 |
| addAF | boolean | Whether or not to add the allele frequencies from gnomAD | true |
| maxAF | numeric | Maximum allele frequency (of the minor allele) cut-off. Variants with AF equal or below this number are considered rare. | 0.001 |
| maxVarFreqCohort | numeric | Maximum variant frequency among the cohort. | 0.05 |
| qcVcf | character | Full path to the vcf file used for VCF-BAM matching. Refer to Files to download. | /path/to/qc_vcf.vcf.gz |
| qcGroups | list | Same as “groups”, but for the VCF-BAM matching | # see aberrant expression example |
Modularization of DROP¶
DROP allows to control which modules to run via the run variable in the config file. By default, each module is set to run: true. Setting this value to false stops a particular module from being run. This will be noted as a warning at the beginning of the snakemake run, and the corresponding module will be renamed in the Scripts/ directory.
For example, if the AberrantExpression module is set to false, the Scripts/AberrantExpression/ directory will be renamed to Scripts/_AberrantExpression/ which tells DROP not to execute this module.
Creating the sample annotation table¶
For a detailed explanation of the columns of the sample annotation, please refer to Box 3 of the DROP manuscript.
Each row of the sample annotation table corresponds to a unique pair of RNA and DNA
samples derived from the same individual. An RNA assay can belong to one or more DNA
assays, and vice-versa. If so, they must be specified in different rows. The required
columns are RNA_ID, RNA_BAM_FILE and DROP_GROUP, plus other module-specific
ones (see DROP manuscript).
The following columns describe the RNA-seq experimental setup:
PAIRED_END, STRAND, COUNT_MODE and COUNT_OVERLAPS. They affect the
counting procedures of the aberrant expression and splicing modules. For a detailed
explanation, refer to the documentation of HTSeq.
To run the MAE module, the columns DNA_ID and DNA_VCF_FILE are needed.
In case external counts are included, add a new row for each sample from those
files (or a subset if not all samples are needed). Add the columns: GENE_COUNTS_FILE,
GENE_ANNOTATON, SPLIT_COUNTS_FILE and NON_SPLIT_COUNTS_FILE. See examples below.
In case RNA-seq BAM files belong to different genome assemblies (eg, ncbi, ucsc), multiple reference genome fasta files can be specified. Add a column called GENOME that contains, for each sample, the key from the genome parameter in the config file that matches its genome assembly (eg, ncbi or ucsc).
The sample annotation file must be saved in the tab-separated values (tsv) format. The column order does not matter. Also, it does not matter where it is stored, as the path is specified in the config file. Here we provide some examples on how to deal with certain situations. For simplicity, we do not include all possible columns in the examples.
Example of RNA replicates¶
| RNA_ID | DNA_ID | DROP_GROUP | RNA_BAM_FILE | DNA_VCF_FILE |
|---|---|---|---|---|
| S10R_B | S10G | BLOOD | /path/to/S10R_B.BAM | /path/to/S10G.vcf.gz |
| S10R_M | S10G | MUSCLE | /path/to/S10R_M.BAM | /path/to/S10G.vcf.gz |
Example of DNA replicates¶
| RNA_ID | DNA_ID | DROP_GROUP | RNA_BAM_FILE | DNA_VCF_FILE |
|---|---|---|---|---|
| S20R | S20E | WES | /path/to/S20R.BAM | /path/to/S20E.vcf.gz |
| S20R | S20G | WGS | /path/to/S20R.BAM | /path/to/S20G.vcf.gz |
Example of a multi-sample vcf file¶
| RNA_ID | DNA_ID | DROP_GROUP | RNA_BAM_FILE | DNA_VCF_FILE |
|---|---|---|---|---|
| S10R | S10G | WGS | /path/to/S10R.BAM | /path/to/multi_sample.vcf.gz |
| S20R | S20G | WGS | /path/to/S20R.BAM | /path/to/multi_sample.vcf.gz |
External count matrices¶
In case counts from external matrices are to be integrated into the analysis, the file must be specified in the GENE_COUNTS_FILE column. A new row must be added for each sample from the count matrix that should be included in the analysis. An RNA_BAM_FILE must not be specified. The DROP_GROUP of the local and external samples that are to be analyzed together must be the same. Similarly, the GENE_ANNOTATION of the external counts and the key of the geneAnnotation parameter from the config file must match.
| RNA_ID | DNA_ID | DROP_GROUP | RNA_BAM_FILE | GENE_COUNTS_FILE | GENE_ANNOTATION |
|---|---|---|---|---|---|
| S10R | S10G | BLOOD | /path/to/S10R.BAM | ||
| EXT-1R | BLOOD | /path/to/externalCounts.tsv.gz | gencode34 | ||
| EXT-2R | BLOOD | /path/to/externalCounts.tsv.gz | gencode34 |
Files to download¶
Two different files can be downloaded from our public repository.
1. VCF file containing different positions to be used to match DNA with RNA files.
The file name is qc_vcf_1000G_{genome_build}.vcf.gz. One file is available for each
genome build (hg19/hs37d5 and hg38/GRCh38). Download it together with the corresponding .tbi file.
Indicate the full path to the vcf file in the qcVcf key in the mono-allelic expression dictionary.
This file is only needed for the MAE module. Otherwise, write null in the qcVcf key.
2. Text file containing the relations between genes and phenotypes encoded as HPO terms.
The file name is hpo_genes.tsv.gz.
Download it and indicate the full path to it in the hpoFile key.
The file is only needed in case HPO terms are specified in the sample annotation.
Otherwise, write null in the hpoFile key.
Advanced options¶
A local copy of DROP can be edited and modified for uncovering potential issues or increasing outputs.
For example, the user might want to add new plots to the Summary scripts, or add
additional columns to the results tables.
Also, the number of threads allowed for a computational step can be modified.
Note
DROP needs to be installed from a local directory using pip install -e <path/to/drop-repo>
so that any changes in the code will be available in the next pipeline run
(see Other DROP versions).
Any changes made to the R code need to be updated with drop update in the project directory.
The aberrant expression and splicing modules use a denoising autoencoder to
correct for sample covariation. This process reduces the fitting space to a
dimension smaller than the number of samples N. The encoding dimension is optimized.
We recommend the search space to be at most N/3 for the aberrant expression,
and N/6 for the aberrant splicing case. Nevertheless, the user can specify the
denominator with the parameter maxTestedDimensionProportion.
DROP allows that BAM files from RNA-seq from samples belonging to the same DROP_GROUP were aligned to different genome assemblies from the same build (eg, some to ucsc and others to ncbi, but all to either hg19 or hg38). If so, for the aberrant expression and splicing modules, no special configuration is needed. For the MAE module, the different fasta files must be specified as a dictionary in the genome parameter of the config file, and, for each sample, the corresponding key of the genome dictionary must be specified in the GENOME column of the sample annotation. In additon, DROP allows that BAM files from RNA-seq were aligned to one genome assembly (eg ucsc) and the corresponding VCF files from DNA sequencing to another genome assembly (eg ncbi). If so, the assembly of the reference genome fasta file must correspond to the one of the BAM file from RNA-seq.