STAR+HTSeq gene counts vs STAR+RSEM genes and how to combine isoforms to get the gene counts?
Hi All,
- In our dataset, we observe the STAR+HTSeq counts are almost double for everygene compared to STAR+RSEM counts. Is there an explanation for this and how to interpret it?
ENSG00000179934.6 HTSeq_Counts RSEM_expected_count Ratio(HTSeq/RSEM) SAMPLE1 3350 1849 1.812 SAMPLE2 2668 1535 1.738 SAMPLE3 36 19 1.895 SAMPLE4 2647 1423 1.860 SAMPLE5 3120 1811 1.723 SAMPLE6 3234 1775 1.822 SAMPLE7 677 364 1.860 SAMPLE8 589 329 1.790 SAMPLE9 573 270 2.122 SAMPLE10 662 352 1.881
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1 answer
One possible explanation...check the Aligned.ToTranscriptome.out.bam file. RSEM uses that, and reads that STAR can align and call with htseq-count might not be making it into the transcriptome file. I've seen that myself (in my case, the library prep had artifacts that STAR's aligner didn't mind, but STAR would not put those reads into the transcriptome file, so RSEM could not see them)
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You are probably going to have to put the command lines you used.