I want to check that I understand the output of RSEM correctly. As I understand it the "expected_count" output for each gene is the number of fragment reads that are predicted to map to that "gene."
Read fragments that map to multiple "genes" are not thrown away but their mapping is divided among those "genes." Thus, you would expect most expected_count estimations to be non-integers.
So if a particular "genes" expected_count value was 1215.54 that would mean that RSEM estimates 1215.54 reads mapped to it. Is this correct?
Another question:
Is there any benchmark for what a "good" expected_count would be in terms of assessing whether or not that gene is expressed?
Does this mean that a transcript with an expected_count of say 8 only had 8 fragments map to it? If this is the case it probably isn't expressed, expressed at exceedingly low levels, or the sequencing was data is bad... right?
Thanks for your input.
Read fragments that map to multiple "genes" are not thrown away but their mapping is divided among those "genes." Thus, you would expect most expected_count estimations to be non-integers.
So if a particular "genes" expected_count value was 1215.54 that would mean that RSEM estimates 1215.54 reads mapped to it. Is this correct?
Another question:
Is there any benchmark for what a "good" expected_count would be in terms of assessing whether or not that gene is expressed?
Does this mean that a transcript with an expected_count of say 8 only had 8 fragments map to it? If this is the case it probably isn't expressed, expressed at exceedingly low levels, or the sequencing was data is bad... right?
Thanks for your input.
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