Hi,
We've got the done the RNA-seq of a species (genome is about 3GB), but NO reference genome is available, using pacbio and Illumina. After the RS_IsoSeq and cd-hit analysis, we have redundant full-length transcripts. Now we want to get the quantification using short reads with Iso-*Seq output used as reference. Since we don't have reference genome, several method can be considered:
1. RSEM( bowtie+RSEM)
2. RSEM (bowtie+eXpress)
3. blat +counting reads mapped to full-length transcript
But now I am confused which method is best for the quantification? Or is there any other method to quantify for no-reference species?
Thanks a lot for any apply!
We've got the done the RNA-seq of a species (genome is about 3GB), but NO reference genome is available, using pacbio and Illumina. After the RS_IsoSeq and cd-hit analysis, we have redundant full-length transcripts. Now we want to get the quantification using short reads with Iso-*Seq output used as reference. Since we don't have reference genome, several method can be considered:
1. RSEM( bowtie+RSEM)
2. RSEM (bowtie+eXpress)
3. blat +counting reads mapped to full-length transcript
But now I am confused which method is best for the quantification? Or is there any other method to quantify for no-reference species?
Thanks a lot for any apply!
