Thank you for developing ExploreATE, it runs fast and is convenient to use.
I have a question regarding quant.sf result.
I am a little confused about how the EffectiveLength column is calculated. Sometimes it is longer than the Length value like this one.
scaffold_713:152931:160869:TE_00001149_INT/LTR/Gypsy | 7938 | 10780.234 | 9.701402e+01 | 2342.334
and this one has very short effective length when both TPM and NumReads are high
scaffold_3:37484:37651:TE_00001309_INT/LTR/unknown | 167 | 8.000 | 6.620188e+04 | 1186.168
Could you clarify how the effective length is calculated? Do you recommend filtering the result based on effective length to identify the true transcription of TEs?
Dear ExploreATE developer,
Thank you for developing ExploreATE, it runs fast and is convenient to use. I have a question regarding quant.sf result. I am a little confused about how the EffectiveLength column is calculated. Sometimes it is longer than the Length value like this one.
scaffold_713:152931:160869:TE_00001149_INT/LTR/Gypsy | 7938 | 10780.234 | 9.701402e+01 | 2342.334and this one has very short effective length when both TPM and NumReads are highscaffold_3:37484:37651:TE_00001309_INT/LTR/unknown | 167 | 8.000 | 6.620188e+04 | 1186.168Could you clarify how the effective length is calculated? Do you recommend filtering the result based on effective length to identify the true transcription of TEs?