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RobiNA: Issue on importing count data

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RobiNA: Issue on importing count data
robina tab delimited table exons normalization
Answer
7/7/15 12:34 AM
In my RNAseq experiment, I ran the FastQC, Trimmomatic, and ToptHat2 in the Discovery Environment of iPlant (http://www.iplantcollaborative.org/).
I have obtained count data using the Bam_to_Counts program posted in iPlant's Discovery Environment. The genomic data I used is the Spirodela polyrhiza genome database posted in Phytozome (http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Spolyrhiza_er ). The transcriptome file I used with Bam_to_Counts was Spolyrhiza_290_v2.gene_exons.gff3 Below is a portion of the tab-delimited file I have downloaded from Bam_to_Counts. The data is only from one library. I added the labeling on the first row. Does RobiNA keep track of the exons in a gene, or do I need to merge the counts all together? How does RobiNA do its normalization without knowing the size of the different exons/transcripts?

Chromosome nt_start nt_end Exons Gene GeneID Count
pseudo0 1363 1860 ID=Spipo0G0000100.v2.290.exon.10 Parent=Spipo0G0000100.v2.290 pacid=31508820 2235
pseudo0 2128 2257 ID=Spipo0G0000100.v2.290.exon.9 Parent=Spipo0G0000100.v2.290 pacid=31508820 420
pseudo0 2972 3267 ID=Spipo0G0000100.v2.290.exon.8 Parent=Spipo0G0000100.v2.290 pacid=31508820 955
pseudo0 3449 3877 ID=Spipo0G0000100.v2.290.exon.7 Parent=Spipo0G0000100.v2.290 pacid=31508820 1230
pseudo0 4015 4074 ID=Spipo0G0000100.v2.290.exon.6 Parent=Spipo0G0000100.v2.290 pacid=31508820 236
pseudo0 4535 4688 ID=Spipo0G0000100.v2.290.exon.5 Parent=Spipo0G0000100.v2.290 pacid=31508820 416
pseudo0 4875 4961 ID=Spipo0G0000100.v2.290.exon.4 Parent=Spipo0G0000100.v2.290 pacid=31508820 206
pseudo0 5537 5677 ID=Spipo0G0000100.v2.290.exon.3 Parent=Spipo0G0000100.v2.290 pacid=31508820 278
pseudo0 6025 6152 ID=Spipo0G0000100.v2.290.exon.2 Parent=Spipo0G0000100.v2.290 pacid=31508820 251
pseudo0 6569 7435 ID=Spipo0G0000100.v2.290.exon.1 Parent=Spipo0G0000100.v2.290 pacid=31508820 1484
pseudo0 11291 11675 ID=Spipo0G0000200.v2.290.exon.2 Parent=Spipo0G0000200.v2.290 pacid=31508327 3
pseudo0 11777 12075 ID=Spipo0G0000200.v2.290.exon.1 Parent=Spipo0G0000200.v2.290 pacid=31508327 1
pseudo0 15395 15426 ID=Spipo0G0000300.v2.290.exon.3 Parent=Spipo0G0000300.v2.290 pacid=31509049 0
pseudo0 15536 15663 ID=Spipo0G0000300.v2.290.exon.2 Parent=Spipo0G0000300.v2.290 pacid=31509049 0
pseudo0 17243 17295 ID=Spipo0G0000300.v2.290.exon.1 Parent=Spipo0G0000300.v2.290 pacid=31509049 0