Closed mpoelchau closed 4 years ago
[containing directory] - yeah, this is confusing. Right now this is either BCM_i5k_pilot
or other_species
Is the part "Data source" in metadata still the information of "Submission" column in .tsv file? Should we use "Run" column instead?
Yes, good point - it would be better to use the 'Run' column.
We'll need to add the final output bam file to apollo.
cp path_to_trackList.json path_to_trackList-bak.json
/app/data/[containing directory]/[gggsss]/[assemblyname]/scaffold/analyses/[species]-[genus]-RNA-Seq_[date]_v1.0
./app/data/[containing directory]/[gggsss]/jbrowse/data
will need to have a symlink to/app/data/[containing directory]/[gggsss]/[assemblyname]/scaffold/analyses
. @mpoelchau will probably need to write a one-time script to create the symlinks for all directories, and add this symlink to the organism onboarding workflow.Bam file:
add_bam_track.pl -i path_to_trackList.json -o path_to_trackList.json --bam_url analyses/[genus]-[species]-RNA-Seq_[date]_v1.0/bamfile --label [gggsss]_[assemblyname]_RNA-Seq-alignments_[date] --category 'RNA-Seq/Mapped Reads' --config '{ "metadata": {SEE BAM_METADATA BELOW} }'
Bigwig files:
add_bw_track.pl -i path_to_trackList.json -o path_to_trackList.json --bw_url analyses/[genus]-[species]-RNA-Seq_[date]_v1.0/downsampled-bigwigfile --label [gggsss]_[assemblyname]_RNA-Seq-alignments_[date]_coverage --plot --category 'RNA-Seq/Coverage Plots' --pos_color "#00BFFF" --config '{ "metadata": {SEE BIGWIG_METADATA BELOW} }'
BAM METADATA:
BIGWIG METADATA (this will likely change in the future, but this is a start):