Mapping And Molecular Identification Of Phenotype Causing Mutations 3.0
Visit source
Download RO-CrateReproduce the tutorial analysis at https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/mapping-by-sequencing/tutorial.html
Associated Tutorial
This workflows is part of the tutorial Mapping And Molecular Identification Of Phenotype Causing Mutations, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| A. thaliana TAIR10 ref genome | A. thaliana TAIR10 ref genome | can be obtained from https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas |
|
| aligned reads from Ler mapping strain | aligned reads from Ler mapping strain | as obtained from https://zenodo.org/record/1098034/files/Ler_mapping_strain.bam |
|
| aligned reads from outcrossed F2 pool | aligned reads from outcrossed F2 pool | as obtained from https://zenodo.org/record/1098034/files/outcrossed_F2.bam |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | SnpEff Download | download the SnpEff genome annotation file corresponding to TAIR10 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0 |
| 4 | Replace parts of text | truncate ref genome chromosome names toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1 |
| 5 | MiModD Variant Calling | compute variant call statistics for both samples across the entire genome toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1 |
| 6 | MiModD Extract Variant Sites | extract variants at sites for which at least one sample is not homozygous wildtype toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1 |
| 7 | MiModD NacreousMap | Variant allele frequency-based linkage analysis toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1 |
| 8 | MiModD VCF Filter | get candidates in linked region toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1 |
| 9 | SnpEff | annotate the candidate mutations toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0 |
| 10 | MiModD Report Variants | toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1 |
Version History
3.0 (earliest) Created 25th Jun 2024 at 10:53 by Helena Rasche
Added/updated 4 files
Open
masterba8f2c0
Creators and Submitter
Views: 306 Downloads: 88
Created: 25th Jun 2024 at 10:53
Last updated: 25th Jun 2024 at 10:53
Tags AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: https://galaxy.training
