Hello

I performed RNAseq using a illumina HiSeq2000 on Arabidposis tissues to aquire fastq files. I used fastx tools to trim my fastq file and then generated BAM files using TopHat2/Bowtie2. I then tried to use RobiNA to generate counts per gene/isoform and perform normalisation using EdgeR and DESeq.

Unfortunately after successfully loading the BAM files into the RobiNA, EdgeR/DESeq was unable to annotate the genes/isoforms and then at the results stage the only identifiers are the chromosomes. I've tried using both the transcriptome alingment and genome alingment (with TAIR10 GFF) but i can't get it to quantify the genes/isoforms.

Do you know how i can make it recognise the genes/isoforms when i import BAM files generated in other packages?

Thanks, Richard

Hi Richard,

it would be great if you could send me a (truncated) sample BAM file so that i can investigate
this further.

cheers,
Marc