DaPars_Extract_Anno.py - coordinates in output BED file (and 'Loci' column) are shifted 1 nucleotide from source transcript #8
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SamBryce-Smith
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…R/DaPars2#8). Add note to README
SamBryce-Smith
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Nov 23, 2021
* create DaPars2_snakemake * update workflow * fix generatePathReadcounts * Refactor Dapars2 to enable snakemake run * minor changes * Minor bug fixes * Fix for merging the chromosome files dynamically. Each run is now per sample. Minimal docker dependencies. This version is still unstable. * change genePredToBed and gff3ToGenePred to Linux version * initial commit make identification BED file from dapars results tbls * remove space from fname * Running version that produces sample wise dapars2 results * First successful test run. * working test run using Dapars2_Multi_Sample.py. chr names not hardcoded * Dapars2 dockerfile - test run successful * remove dapars2 scripts from repo * add rulegraph * minimal updates to README (mainly notes) * add bind to test-data dir - fixes new file not found error * remove bed from samples.csv as not used - test run successfuly no errors * update instructions in README and config * update to dockerfile hosted by apaeval * template rule to use utils's gtf2bed12 * remove template files and files unrelated to workflow * simplify workflow. Split into subrules. Use utils gtf2bed12 * update readme and rulegraph * update rule description for mainDapars2 * recover q2 benchmark file * remove dapars2 conda env file * gtf in config points to test_data repo * reorganise readme * Assign read counts as variable before writing. Will enforce rule to stop upon error * add citations, links to repo & docs in README * update comments in run_local.sh * remove commented targets in rule finish in main Snakefile * use public pandas dockerfile for identification_bed. runs on test data * rm configfile declaration in main snakefile. threads defined in config. * use-singularity instead of --use-conda for dryrun.sh * notes in README RE unsorted BED, exclusion from quant & DU challenges * add dapars2 threads declaration to config * -1 on minus strand distal polyA sites to match source tx (address 3UTR/DaPars2#8). Add note to README * add note on how to install conda environment * merge main into DaPars2-snakemake branch Co-authored-by: Pin-Jou Wu <pjwu@Pin-JoudeMacBook-Pro.local> Co-authored-by: Maria Katsantoni <maria.katsadoni@gmail.com> Co-authored-by: Pin-Jou Wu <pinjouwu.tw@gmail.com> Co-authored-by: Farica Zhuang <faricazjj@gmail.com>
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This is a duplicate of ZhengXia/dapars#16 in the DaPars repo, as
DaPars_Extract_Anno.pyis identical between the repos.TL;DR:
+ strand: DaPars BED/'Loci' 3'UTR start is 1 nt downstream of the actual annotated start
- strand: Dapars BED/'Loci' 3'end of the 3'UTR is 1 nt upstream of the actual annotated end
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