RNA class annotation RNASeq

[Dani]

Hi,

I am trying to to this pretty common "quantification" representation of different RNA classes in my RNA-Seq data set (meaning mRNA, tRNA, rRNA, ncRNA etc, like for example here http://journalofextracellularvesicle...#CIT0025_26760), but I can't seem to find any tools that do that - can anybody help with that?

Thanks,

Danielle

[Dani]

Btw. found that biotypes in ngi_visualization does the job if anybody has the same question=)

[Michael.Ante]

Hi Danielle,

I hope it's not to late for a suggestion. The Genecode and ENSEMBL annotations include in their gtf files per gene a field called "gene_biotype".
If you use htseq-count (for instance), you can switch from counting the reads per gene_id to counting the reads per gene_biotype:

 htseq-count -f bam -r pos -i gene_biotype my_alignment.bam my_genecode.gtf

Before doing so, check if the gtf and your bam file base on the same assembly (e.g. hg19) and have the same naming for the chromosomes' name.

Cheers,

Michael

[Dani]

Hi Michael,

that's a great suggestion, thanks - unfortunately, it complains:
Error occured when processing GFF file (line 8 of file /mnt/users/dga
Feature ENSG00000223972.5 does not contain a 'gene_biotype' attribu
[Exception type: ValueError, raised in count.py:53]
I am using: gencode.v25.primary_assembly.annotation.gtf which has the same assembly and naming as my bam.
Does that mean that the gtf files have to be "cleaned" up to not contain any empty biotypes before using?

Thanks,

Danielle

[Dani]

Sorry, realized that it should be -i gene_type =)