Description | Location |
---|---|
identify relevant TCGA WXS and RNAseq | http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/identify_TCGA_WGS_runs.ipynb |
input | output | |
---|---|---|
raw bams from TCGA website | allelic read counts | http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/TestPipeline/submitJobForAllleleExtraction.ipynb |
TCGA website | preprocessed TCGA VCF files | http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/downloadingVCFs.ipynb |
TCGA website | VCF metadata annotations | http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/Pull_TCGA_meta_data.ipynb |
preprocessed TCGA VCF files | merged VCF file | http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/mergeTCGA_VCF.ipynb# |
reprocessed bam-reacount out files | merged bam-reacount out file | http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/TestPipeline/mergeBamReadCountFiles.ipynb |
Description | Location |
---|---|
calling mutation in TCGA using simple allelic read counts with less than 10 lines | http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/TestPipeline/mutationCalling.ipynb# |
analyze RNA-seq and WXS allelic read count concordance | http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/Compare_TCGA_RNAseq_WXS.ipynb |
The URL locations are hardcoded for me clicking to go to different notebooks.
Find TCGA WXS runs http://localhost:6001/notebooks/Project/METAMAP/notebook/RapMapTest/XGS_WGS/identify_TCGA_WGS_runs.ipynb
check for TCGA aligning speed:
http://localhost:6001/edit/Project/METAMAP/notebook/RapMapTest/XGS_WGS/TestPipeline/align_tcga.py