Question: What impact does sorting by read name have on RSEM abundance estimates
gravatar for adam.faranda
13 months ago by
adam.faranda80 wrote:

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.

rsem rna-seq tools • 257 views
ADD COMMENTlink written 13 months ago by adam.faranda80
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1496 users visited in the last hour