diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/404.html b/404.html new file mode 100644 index 0000000..0ba5ae8 --- /dev/null +++ b/404.html @@ -0,0 +1,383 @@ + + + +
+ + + + + + + + + + + + + + +and welcome to the TreeVal Curation workshop
+I'm Damon and i'll be going through the vast majority of this workshop with you.
+Yumi will be here answering the questions I can't, and Will will be in the chat.
+We have put alot of work into TreeVal so hopefully you'll find it incredibly helpful for your own project. Keep in mind that this course does run with the hope you attend the workshop by GRIT, who will show you how this data is used and how to manually curate your genome.
+1, We will be using GitPod for this tutorial so SEND ME TO GITPOD!.
+2, The Nextflow command:
+nextflow_cmd run treeval/main.nf \
+-profile singularity \
+--input treeval/assets/local_testing/nxOscDF5033-BGA.yaml \
+--outdir OscDF5033-TEST \
+-entry RAPID
+
nextflow
, however, we had an issue with adding nextflow to path.3, Uploading to JBrowse
+cd jbrowse2
+
+jbrowse add-assembly /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/ilTolViri5_1.fa -a ilTor --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/ilTolViri5_1_ancestral.bigBed -a ilTor -n ancestral_busco --category Busco --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/ilTolViri5_1_buscogene.bigBed -a ilTor -n standard_busco --category Busco --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/ilTolViri5_1_selfcomp.bigBed -a ilTor -n selfcomp --category selfcomp --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/telo_ilTolViri5_1.bed.gz -a ilTor -n telomere --category Alignments --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/gap_ilTolViri5_1.bed.gz -a ilTor -n gap --category Alignments --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/BSPQI.bigBed -a ilTor -n BSPQI --category Enzymes_Digest --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/BSSSI.bigBed -a ilTor -n BSSSI --category Enzymes_Digest --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/DLE1.bigBed -a ilTor -n DLE1 --category Enzymes_Digest --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/hic_files/ilTolViri5_1.hic -a ilTor -n HIC --category Mapping --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/DanausPlexippus.Dpv3_pep.gff.gz -a ilTor -n DanPlexPeptide --category Alignments --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/DanausPlexippus.Dpv3_cdna.bigBed -a ilTor -n DanPlexCDNA --category Alignments --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/DanausPlexippus.Dpv3_cds.bigBed -a ilTor -n DanPlexCDS --category Alignments --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/DanausPlexippus.Dpv3_rna.bigBed -a ilTor -n DanPlexRNA --category Alignments --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/MelitaeaCinxia.ilMelCinx1_pep.gff.gz -a ilTor -n MelCinPEP --category Alignments --load copy
+
+jbrowse add-track /workspace/treeval-curation/ilTorViri5-BGA/treeval_upload/HeliconiusMelpomene.ASM31383v2_cdna.bigBed -a ilTor -n HelMelPEP --category Alignments --load copy
+
+cd ../
+
4, Uploading to Higlass
+You will have to close any current higlass tabs you have open, navigate to the gitpod window, ports and open a new higlass window.
+cd /workspace/treeval-curation/ilTorViri5-BGA/hic_files/
+
+cp {ilTolViri5_1.mcool,../treeval_upload/ilTolViri5_1.genome,ilTolViri5_1_coverage.bigWig,ilTolViri5_1_repeat_density.bigWig,ilTolViri5_1_gap.bed,ilTolViri5_1_telomere.bed} /tmp/higlass-docker/
+
+cd ../../
+
+higlass-manage ingest /tmp/higlass-docker/ilTolViri5_1.mcool --assembly ilTorViri5_1 --project-name TreeVal-test
+
+higlass-manage ingest --filetype chromsizes-tsv --datatype chromsizes --assembly ilTorViri5_1 /tmp/higlass-docker/ilTolViri5_1.genome --project-name TreeVal-test
+
+higlass-manage ingest /tmp/higlass-docker/ilTolViri5_1_coverage.bigWig --assembly ilTorViri5_1 --project-name TreeVal-test
+
+higlass-manage ingest /tmp/higlass-docker/ilTolViri5_1_repeat_density.bigWig --assembly ilTorViri5_1 --project-name TreeVal-test
+
+clodius aggregate bedfile --chromsizes-filename /tmp/higlass-docker/ilTolViri5_1.genome /tmp/higlass-docker/ilTolViri5_1_gap.bed
+
+higlass-manage ingest /tmp/higlass-docker/ilTolViri5_1_gap.bed.beddb --datatype bedlike --filetype beddb --assembly ilTorViri5_1 --project-name TreeVal-test
+
+clodius aggregate bedfile --chromsizes-filename /tmp/higlass-docker/ilTolViri5_1.genome /tmp/higlass-docker/ilTolViri5_1_telomere.bed
+
+higlass-manage ingest /tmp/higlass-docker/ilTolViri5_1_telomere.bed.beddb --datatype bedlike --filetype beddb --assembly ilTorViri5_1 --project-name TreeVal-test
+
5, CurationPretext
+This pipeline can be run like such:
+nextflow_cmd run curationpretext/main.nf -profile singularity --input /workspace/treeval-curation/Oscheius_DF5033/genomic_data/Oscheius_DF5033.fa --pacbio /workspace/treeval-curation/Oscheius_DF5033/pacbio/ --cram /workspace/treeval-curation/Oscheius_DF5033/hic-arima2/ --outdir pretext_full -entry ALL_FILES
+
nextflow_cmd run curationpretext/main.nf -profile singularity --input /workspace/treeval-curation/Oscheius_DF5033/genomic_data/Oscheius_DF5033.fa --cram /workspace/treeval-curation/Oscheius_DF5033/hic-arima2 --outdir pretext_maps -entry MAPS_ONLY
+