Hi-
I am trying to fully understand the effective length calculation for RSEM.
My understanding was that it was as follows:
'length' is this transcript's sequence length (poly(A) tail is not counted). 'effective_length' counts only the positions that can generate a valid fragment. If no poly(A) tail is added, 'effective_length' is equal to transcript length - mean fragment length + 1. If one transcript's effective length is less than 1, this transcript's both effective length and abundance estimates are set to 0.
However, if I look at my data (no poly(A) tail added), I find that for most transcripts, the difference between transcript length and effective length is 85 (which generally makes sense for my data). However, for shorter transcripts, it seems to vary.
I understand that when the effective length would end up being less than 0, it gets set to 0. But in my case, it does vary for these smaller transcripts.
Thanks in advance for your help!
--Matt Newman
transcript_id |
gene_id |
length |
effective_length |
expected_count |
TPM |
FPKM |
IsoPct |
|
NR_003498_chr15 |
HBII-52-45_chr15 |
53 |
1.02 |
0 |
0 |
0 |
0 |
51.98 |
NR_036157_chr19 |
MIR320E_chr19 |
53 |
1.02 |
0 |
0 |
0 |
0 |
51.98 |
NR_036093_chr7 |
MIR548T_chr7 |
53 |
1.02 |
0 |
0 |
0 |
0 |
51.98 |
NR_031740_chr1 |
MIR1976_chr1 |
52 |
0 |
0 |
0 |
0 |
0 |
52 |
NR_036172_chr22 |
MIR3201_chr22 |
52 |
0 |
0 |
0 |
0 |
0 |
52 |
NR_031694_chr22 |
MIR1281_chr22 |
54 |
1.12 |
0 |
0 |
0 |
0 |
52.88 |
NR_036226_chr2 |
MIR4262_chr2 |
54 |
1.12 |
0 |
0 |
0 |
0 |
52.88 |
NR_003944_chr1 |
SNORD78_chr1 |
54 |
1.12 |
0 |
0 |
0 |
0 |
52.88 |
NR_030386_chr20 |
MIR663_chr20 |
93 |
11.06 |
0 |
0 |
0 |
0 |
81.94 |
NR_036144_chr16 |
MIR3180-3_chr16 |
94 |
11.5 |
0 |
0 |
0 |
0 |
82.5
|
NR_030294_chr3 |
MIR551B_chr3 |
96 |
12.41 |
0 |
0 |
0 |
0 |
83.59 |
NR_015380_chr19 |
A1BG-AS1_chr19 |
2130 |
2045 |
0 |
0 |
0 |
0 |
85 |
NM_130786_chr19 |
A1BG_chr19 |
1766 |
1681 |
0 |
0 |
0 |
0 |
85 |
NM_001198818_chr10 |
A1CF_chr10 |
9362 |
9277 |
0 |
0 |
0 |
0 |
85 |
NM_001198819_chr10 |
A1CF_chr10 |
9529 |
9444 |
0 |
0 |
0 |
0 |
85 |
NM_001198820_chr10 |
A1CF_chr10 |
9412 |
9327 |
0 |
0 |
0 |
0 |
85 |
NM_014576_chr10 |
A1CF_chr10 |
9269 |
9184 |
0 |
0 |
0 |
0 |
85 |
NM_138932_chr10 |
A1CF_chr10 |
9293 |
9208 |
0 |
0 |
0 |
0 |
85 |
NM_138933_chr10 |
A1CF_chr10 |
9364 |
9279 |
0 |
0 |
0 |
0 |
85 |