Jbrowse configuration file for specific usage

Question

[misko.cervenansky]

Hello, i am looking for help with visualization of my files from Chado database in Jbrowse. I am using biodb-to-json.pl but i am not able to write configuration file that suits my need. I am going for view like in volvox test data, but i also need name labels for subfeatures. I am able to get close to this using subfeatures, or subparts, but i have no idea how to enable subfeature name labels. If i use just everything as features i am getting all the information i need, but i would like it in nicely in one row. Thanks for your time, appreciating any help.

Yours sincerely Michal.

[cmdcolin]

Can you describe exactly what you are looking for? What about your data screenshot is incorrect? Does your data contain subfeatures and parent features? What do you mean by "subfeature name labels"? Definitely encourage posting on jbrowse github or jbrowse mailing list just since we don't always see jbrowse questions from this forum :)

[finswimmer]

Hello misko.cervenansky!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=83117

This is typically not recommended as it runs the risk of annoying people in both communities.

You should at least mention where you posted your question also.

[colindaven]

Do you mean that you want subfeature labels such as exons to be displayed ? I've never seen this done before. Are you sure the exon labels are also present in the database ? Using GFF3, I have seen labels such as ID, Name, Description and Note to be displayed slightly differently, experimentation is highly recommended.

As far as I know, the volvox sample data are prepared from a GFF3 and or GTF, so this might be dealt with differently. Could be wrong though. I have never used a Chado D I'm afraid.

Using GFF3 or GTF, I think JBrowse can only deal with one subfeature type per feature. I generally use mRNA as feature (not gene) and exon as subfeature.

Answer 1

[colindaven]

For what it's worth, here's my script which inserts subfeatures from (properly formatted) GFF3.

## Add tracks to JBrowse and print all subfeatures eg CDS and exons separately. 
## You must be in the same directory 


## Now supply the following GFF3 variable on the command line as argument 1, sh addJBrowseSubfeatures3.sh file.gff3
echo "Input file: " $1
gff_name=$1

## Do not change this paragraph
origDir=$(pwd)
jbrowse="/var/www/html/JBrowse/"
cd $jbrowse
pwd

gff3_file=$origDir"/"$gff_name

## Uncomment the (only one) JBrowse instance directory you want to add data with to.
#outdir="galaxy_nfs/jbdata/hg19_hg"
#outdir="galaxy_nfs/jbdata/GRCh38_hg"
#outdir="galaxy_nfs/jbdata/hg19_cell/"
#outdir="galaxy_nfs/jbdata/GRCh38_noalt_friel/"
#outdir="galaxy_nfs/jbdata/Rat_RN6"
#outdir="galaxy_nfs/jbdata/mm9"
#outdir="galaxy_nfs/jbdata/mm10"
#outdir="galaxy_nfs/jbdata/Zeb_GRCz10"
#outdir="galaxy_nfs/jbdata/mg17_5"
#outdir="galaxy_nfs/jbdata/PAO1"
#outdir="galaxy_nfs/jbdata/PA14"


# Do not change this
bin/flatfile-to-json.pl \
        --trackLabel $gff_name \
        --gff $gff3_file \
        --out $outdir \
        --key $gff_name  \
        --className transcript \
        --type mRNA \
        --autocomplete all \
        --getSubfeatures \
        --subfeatureClasses '{"exon":"exon","CDS":"transcript-CDS"}' \
        --arrowheadClass 'arrowhead' \
;


#       --subfeatureClasses '{"mRNA":"mRNA","exon":"exon","CDS":"CDS"}' \
#       --subfeatureClasses '{"mRNA" : "mRNA", "exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' \