Add OGSv1.2 to Oncopeltus fasciatus private haplotype browsers

[mpoelchau]

OGS v1.2 is here: https://i5k.nal.usda.gov/bio_data/836678

The community wants to review these assemblies, and having the OGS on each haplotype will likely help. The OGS will need to be remapped first.

[mpoelchau]

Can you also add (these are gff3s so you can use liftoff):

• Extavour Maternal and early embryonic 454 transcriptome: https://i5k.nal.usda.gov/data/Arthropoda/oncfas-%28Oncopeltus_fasciatus%29/BCM-After-Atlas/4.Transcriptomes%20and%20RNA-Seq/Maternal_and_early_embryonic_transcriptome/
• Benoit Trinity transcriptome: https://i5k.nal.usda.gov/data/Arthropoda/oncfas-%28Oncopeltus_fasciatus%29/BCM-After-Atlas/4.Transcriptomes%20and%20RNA-Seq/Benoit_Trinity_transcriptome/

[amcooksey]

added OGS (new version is 1.3) and 454 and Trinity transcriptome tracks to Apollo

[mpoelchau]

Thanks @amcooksey! Can you update the metadata for the transcriptome tracks:

Track 1, hap1:

• category: RNA-Seq/Assembly
• Name: Lifted Maternal and early embryonic 454 transcriptome
• Metadata:
  • Publication: Ewen-Campen B., Shaner N., Panfilio K. A., Suzuki Y., Roth S., and Extavour C. G. (2011). The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 12: 61.
  • Data source: PRJNA79671; Accession #s SRX022011, SRX022012, SRX022013, SRX022014; https://i5k.nal.usda.gov/data/Arthropoda/oncfas-%28Oncopeltus_fasciatus%29/BCM-After-Atlas/4.Transcriptomes%20and%20RNA-Seq/Maternal_and_early_embryonic_transcriptome/
  • Analysis: LiftOff v1.6.3. 125,550 genes out of 149,438 genes were lifted over.

Track 1, hap2:

• category: RNA-Seq/Assembly
• Name: Lifted Maternal and early embryonic 454 transcriptome
• Metadata:
  • Publication: Ewen-Campen B., Shaner N., Panfilio K. A., Suzuki Y., Roth S., and Extavour C. G. (2011). The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics 12: 61.
  • Data source: PRJNA79671; Accession #s SRX022011, SRX022012, SRX022013, SRX022014; https://i5k.nal.usda.gov/data/Arthropoda/oncfas-%28Oncopeltus_fasciatus%29/BCM-After-Atlas/4.Transcriptomes%20and%20RNA-Seq/Maternal_and_early_embryonic_transcriptome/
  • Analysis: LiftOff v1.6.3. 112,354 genes out of 149,438 genes were lifted over.

Track 2, hap 1:

• category: RNA-Seq/Assembly
• Name: Lifted Benoit Trinity transcriptome
• Metadata:
  • Data source: https://i5k.nal.usda.gov/data/Arthropoda/oncfas-%28Oncopeltus_fasciatus%29/BCM-After-Atlas/4.Transcriptomes%20and%20RNA-Seq/Benoit_Trinity_transcriptome/
  • Analysis: LiftOff v1.6.3. 30,785 out of 31,458 genes were lifted over.

Track 2, hap 2:

• category: RNA-Seq/Assembly
• Name: Lifted Benoit Trinity transcriptome
• Metadata:
  • Data source: https://i5k.nal.usda.gov/data/Arthropoda/oncfas-%28Oncopeltus_fasciatus%29/BCM-After-Atlas/4.Transcriptomes%20and%20RNA-Seq/Benoit_Trinity_transcriptome/
  • Analysis: LiftOff v1.6.3. 28,177 out of 31,458 genes were lifted over.

[mpoelchau]

For the OGS, can you:

• copy the jbrowse/data/names directory from scinet to Apollo - run_flatfile2json.sh should index the names for you, we just need the directory available
• update the metadata:
  • Data source: https://i5k.nal.usda.gov/data/Arthropoda/oncfas-%28Oncopeltus_fasciatus%29/BCM-After-Atlas/2.Official%20or%20Primary%20Gene%20Set/OGS_v1.2/oncfas_OGSv1.2_02192016/
  • Analysis: LiftOff v1.6.3

[amcooksey]

for the OGS, the jbrowse/data/names directory is already there. I ran flatfiletojson.sh on scinet already. do I need to run it again?

[amcooksey]

updated metadata

[mpoelchau]

ah okay. The name index wasn't working so I assumed the directory hadn't been updated. Instead it looks like it only has indexes for the Lifted Maternal and early embryonic 454 transcriptome. You could just run the name indexing part on its own and just specify the OGS (no need to index the transcriptome tracks). It might be possible to just run flatfile2json.sh on the OGS track (not sure if it will create a duplicate track though).

[amcooksey]

updated OGS 1.3 indexing