I'm new to RNA-Seq analysis and have Illumina HiSeq paired-end reads (100bp) from plant samples. I would like to get a count of read abundance on the isoform as well as gene level and to proceed to DESeq for differential expression. I've been reading that HTseq is a suitable tool for obtaining read counts (as opposed to RSEM which gives estimates instead of actual counts).
My problem is that there is no reference genome for my plant species, and I notice that most examples for HTseq are for samples with reference genomes with known gene annotations. Can I still use HTseq for obtaining read count values if no reference genome is available?
Thanks in advance for any advice.
My problem is that there is no reference genome for my plant species, and I notice that most examples for HTseq are for samples with reference genomes with known gene annotations. Can I still use HTseq for obtaining read count values if no reference genome is available?
Thanks in advance for any advice.
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