What impact does sorting by read name have on RSEM abundance estimates
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2.9 years ago
adam.faranda ▴ 90

The RSEM utility "rsem-calculate-expression" has a setting "--sort-bam-by-read-name". The documentation states that doing so will result in deterministic maximum likelihood estimates, at the cost of longer run-times and larger memory requirements. By default, this setting is disabled

Given the same set of input data files (reads and RSEM Reference) does RSEM calculate the same Estimated Counts / TPM / FPKM over multiple repeated runs without this setting enabled?

I am currently running a repeat on my data set (using default RSEM Settings) to compare A vs. B; I was hoping someone with RSEM experience could comment on how this setting impacts RSEM results.

RNA-Seq Tools RSEM • 555 views

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