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COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
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transcript with very small EffectiveLength #921

Open steven-bioinfo opened 8 months ago

steven-bioinfo commented 8 months ago

Hello,

I use salmon to analyse my metatranscriptomic data.

In my results I found, some very high TPM but this TPM have already a very small EffectiveLength. Because of this very small EffectiveLength, the TPM are very high (and less reproducible between my replicates).

How to analyse this TPM ? It's possible to remove this bias with a salmon argument ?

command line : 

salmon quant -i {input.salmon_index} -l A -1 {input.fastq_1} -2 {input.fastq_2}  --validateMappings -o {params.output_dir} --meta -p {threads} --seqBias --gcBias

Exemple of Top3 TPM on a sample : 

Name    Length  EffectiveLength TPM NumReads
lcl|NC_001136.10_cds_NP_010562.1_1187   168 8.000   27437.393774    1808.000
lcl|NC_001145.3_cds_NP_013978.1_4507    180 13.000  80351.033367    8604.000
lcl|NC_001137.3_cds_NP_010898.1_1506    132 1.000   85468.695651    704.000

Thanks,

Steven