Expression and Quantification

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A sleuth for RNA-Seq

A sleuth for RNA-Seq

from Bits of DNA by Lior Pachter Today my student Harold Pimentel released the beta version of his new RNA-Seq analysis method and software program called sleuth. A sleuth for RNA-Seq begins with the quantification of samples with kallisto, and together a sleuth ...

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RPKM, FPKM and TPM, clearly explained

RPKM, FPKM and TPM, clearly explained

from StatQuest It used to be when you did RNA-seq, you reported your results in RPKM (Reads Per Kilobase Million) or FPKM (Fragments Per Kilobase Million). However, TPM (Transcripts Per Kilobase Million) is now becoming quite popular. Since there seems ...

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LFC – a count ratio model to estimate fold changes

LFC – a count ratio model to estimate fold changes

Various biases affect high-throughput sequencing read counts. Contrary to the general assumption, researchers from Ludwig-Maximilians-University Munich show that bias does not always cancel out when fold changes are computed and that bias affects more than 20% of genes that are ...

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