Salmon, Getting New TPM from new, updated NumReads
Hello, I have recently normalized my read counts (NumReads in Salmon output) and I would like to get the new updated TPMs using these Numreads counts. Is there a method I could go around doing this? The effective length and length would be the same regardless. I have all of the same data available, just with different NumReads now. Knowing how Salmon gets TPM counts would be beneficial as well. Thank you!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Mapping vs Alignment mode in Salmon
written by Sowmya •
-
Salmon and SPAdes contigs filtering
written by Skeetul •
-
Counts vs TPM - Comparing gene expression within a sample
written by jac •
-
TPM for scRNAseq
written by little_more •
-
Tximport "sclaedTPMs" imports NumReads column from Salmon output
written by anna •
-
how to interpret very short effective length in Salmon output
written by hans •
-
Transcript level counts from full length scRNA data
written by GouthamAtla
-
Using Mann-Whitney U Test to compare replicates
written by jjrin •
-
Transcripts ID matching in tximport for edgeR
written by Sharon
-
Gene annotation and sequence download in Mycobacterium tuberculosis H37Rv
written by Ritvik •
Decent explanation of the units: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/
R script for conversion:
binary for conversion: https://github.com/mforde84/tpmcalc