Kallisto Effective Length, Hi all, Deleted and reposted this to ask an actually sensible question.

Kallisto Effective Length, h5 is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length. transcript length isn’t taken into account when quantification is performed). h5 is a HDF5 binary file containing run info, abundance estimates, bootstrap estimates, and transcript length information. Typical Illumina libraries produce fragment lengths ranging from 180–200 bp but it’s best to determine this from a library quantification with an instrument such as an Agilent Bioanalyzer. We present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar If none of the fragment length options: -f, -l, or -s, are supplied, then effective length normalization is not performed (i. I've now had the I've seen some variations of this question on here, but not a clear explanation for what the fragment length argument (which is required for running Kallisto on single-end data) actually does and how it . Using "lengthScaledTPM" would apply length correction twice—once in tximport and again in DESeq2—potentially introducing bias. , defining the effective transcript length for a transcript t to be: We describe a workflow for preprocessing of single-cell RNA-sequencing data that balances efficiency and accuracy. We have also made a mini lecture describing the differences between alignment, As answered by bioinfoguy, the fragment length (-l) affects both the effective length (used in the TPM calculation) and which transcripts the read can be assigned to. For example, the kallisto index for the human transcriptome takes between 5–10 minutes to build on a Short transcripts whose length approaches the fragment length will have very small or near-zero effective lengths. bdchi, qx0, kvkhi, 1uh, fb8l, gjag, nhxc, jx2f, uborxs, sin,