Baltica project configuration¶
Baltica requires a project configuration file as input. For a template see here. For a programmatic solution to generate the configuration, use the script baltica/write_new_config.R. Method specific parameters are detailed in the Workflow implementation page.
Warning
Baltica project requires that configuration been update.
Users should use the full path to files.
The sample names for the samples parameters uses a underscore (_) to separate the sample name and replicate number, like in mix_1, so the sample should not contain spaces or underscores.
Note
The Required column flags parameters without a default value.
General parameters description¶
| Parameter | Description | Required |
|---|---|---|
| path | project path | ✓ |
| sample_path | path to the parent directory for aligment files | ✓ |
| samples | sample name and directory formated as "{sample_name}: {path_to_sample) | ✓ |
| contrasts | list of contrasts names (format) | ✓ |
| assembly | assembly name on UCSC Browser | |
| strandness | one of fr-firststrand, fr-secondstrand or none (unstranded) | ✓ |
| read_len | maximun read length | ✓ |
| ref | path to reference annotation in the GTF format | ✓ |
| ref_fa | path to reference annotation in the FASTA format | ✓ |
| project_authors | project author name, used in the report | |
| project_title | project title name, used in file names and report | |
| orthogonal_result | path to results from orthonal experiment, such as ONT RNA-seq (see) | |
| baltica_max_table | maximum number of rows for the Baltica table in the HTML report |
Pairwise comparisons¶
contrasts:
{case1}-vs-{control}:
- {case1}
- {control}
{cas2}-vs-{control}:
- {case2}
- {control}
Note
junctionseq and leafcutter support more complex experimental designs, which were not implemented in Baltica.
Orthogonal result¶
Full path to GFF or BED with a valid score column. Optionally a comparison or name column containing the experimental comparisons. Otherwise, only the first contrast of the project is used. This parameter allows Baltica to integrate a validation dataset obtained with third-generation sequencing.
majiq specific paramers¶
| Parameter | Original parameter | Description |
|---|---|---|
rule majiq_build: (majiq deltapsi) |
||
| majiq_min_experiments | --min-experiments | minimum number of experiments to filter with --minreads (default 1.0 - all experiments) |
| majiq_minreads | --minreads | Discard SJ with less than --minreads reads |
| majiq_min_denovo | --min-denovo | Discard novel SJ with less than --min-denovo reads |
rule majiq_deltapsi (majiq deltapsi) |
||
| majiq_minreads | --minreads | same as above |
rule majiq_voila (voila tsv) |
||
| majiq_non_changing_threshold | --non-changing-threshold | |
| majiq_threshold | --threshold |
junctionseq specific paramers¶
qorts manual junctionseq manual
| Parameter | Original parameter | Description |
|---|---|---|
rule junctionseq_qc (qorts QC) |
||
| is_single_end | --singleEnded | Flag single end libraries |
rule junctionseq_merge (qorts mergeNovelSplices) |
||
| junctionseq_mincount | --minCount | Discard SJ with less than --minCount reads |
leafcutter specific paramers¶
regtools manual leafcutter manual
| Parameter | Original parameter | Description |
|---|---|---|
rule leafcutter_bam2junc (regtools junctions extract) |
||
| leafcutter_minimum_anchor_length | -a | Discard reads with overanging length lower than -a |
| leafcutter_minimum_intron_size | -i | Minimum intron size |
| leafcutter_maximum_intron_size | -I | Maximum intron size |
| rule leafcutter_differential_splicing | ||
| leafcutter_min_coverage | --min_coverage | desc |
| leafcutter_min_samples_per_group | -g | Discard SJ used in less than -g samples |
| leafcutter_min_samples_per_intron | -i | Discard SJ with less than --min_coverage in -i samples in each group |
rmats specific paramers¶
| Parameter | original parameter | Description |
|---|---|---|
rule rmats_run (rmats.py) |
||
| rmats_allow_clipping | --allow-clipping | Allow clipped reads |
| rmats_variable_read_length | --variable-read-length | Allow reads with variable-length |
| rmats_novel_ss | --novelSS | Allow the detecting unannotated SJ |
| rmats_extra | none | Pass extra arguments to rmats.py |