RNA-seq transcriptome visualization

[id0]

RNA-seq reads are mapped to the genomic coordinates and then visualized in something like IGV or UCSC Genome Browser. However, all viewers seem to include introns in the output. For smaller genes, this is fine, but for genes with a lot of introns and/or large introns, this becomes more difficult.

Is there a tool that can take out introns for visualizing transcriptome data? I'd like to see coverage across the entire gene without all the unnecessary gaps. Is that possible?

[Wallysb01]

You could just do the alignment to only the transcriptome, as created from the annotation file you give tophat for example. Then use that transcriptome fasta file as the reference genome in IGV and keep the aligned reads bam file to that transcriptome.

You could also just pick up at this spot in the Trinity package: http://trinityrnaseq.sourceforge.net...zation_QC.html

Just use the transcriptome as created from the annotation file as what would be the trinity assembly (Trinity.fasta) there.

[id0]

You could just do the alignment to only the transcriptome, as created from the annotation file you give tophat for example. Then use that transcriptome fasta file as the reference genome in IGV and keep the aligned reads bam file to that transcriptome.

You could also just pick up at this spot in the Trinity package: http://trinityrnaseq.sourceforge.net...zation_QC.html

Just use the transcriptome as created from the annotation file as what would be the trinity assembly (Trinity.fasta) there.

I thought about that. I already have the BAMs and may necessarily not have the option to go back to FASTQs.

Also, this way, I don't get exon boundaries or amino acids.

[Wallysb01]

Yeah, I don’t know how you’ll keep exon boundaries. It sounds like you just want to visually “shorten” introns, but other than some crafty photoshop work, I don’t know how that’s going to happen.

And you should be able to do a BAM to fastq file conversation. Assuming the BAM file hasn’t been filtered and contains unaligned reads, you should have all the reads there.