Question: How to obtain transcript level TPM using stringtie?
0
Entering edit mode
3 months ago
kousi31 • 0

Hi all,

Stringtie reports TPM at gene level, but I need TPM at transcript level. Is there a way to obtain transcript level TPM using stringtie?

ADD COMMENTlink 3 months ago kousi31 • 0 • updated 3 months ago ruisergioluis • 20
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Entering edit mode
3 months ago
manuel.belmadani • 830
Canada

It does provide transcript level TPM since 2015:

10/19/2015 - v1.1.0 release This StringTie release includes the following updates: major memory usage improvements due to: changes of internal data structures, collapsing reads aligned in the same place and filtering of spurious spliced alignments within large bundles -- most RNA-seq data samples use much less than 1Gb of memory now. TPM is now also reported for transcripts and genes (besides FPKM)

Also from https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual:

for each RNA-Seq sample, run StringTie using the -B/-b and -e options in order to estimate transcript abundances and generate read coverage tables for Ballgown.

ADD COMMENTlink 3 months ago manuel.belmadani • 830
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Entering edit mode
3 months ago
ruisergioluis • 20

The TPMs values are located in the GTF file, returned by StringTie. If you want a simple two-column file with Transcript ID and TPM, you can simply run the following command:

grep -P "\ttranscript\t"  StringTie_sampleName.gtf  | cut -f9 | awk '{gsub("\"","",$0);gsub(";","",$0);print $4,$12}'

I didn't test it but should be fine.

ADD COMMENTlink 3 months ago ruisergioluis • 20

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