Unable to create file for tximport

Question

[ankur]

Hello there, I am new to RNA seq analysis, so please excuse me for this basic question. Since one week I am trying to import my StringTie reestimation results via tximport tool so that I can use it for DESeq2 tool. But I am unable to understand how exactly I can create my 'files' and import it.

My StringTie results contain for every sample e2t.ctab e_data.ctab i2t.ctab i_data.ctab SRR12345.gtf t_data.ctab

The manual which I am following is tximport here they have not given how one can use the data from StringTie results. Can anyone please guide me how I can create files and which files i can use from StringTie reestimation

Thank You in advance.

[Bastien Hervé]

7/21/2016

• using DESeq2 and edgeR with StringTie's output Thanks to a productive summer internship of high school student David Miller there is now a script available for converting the output of StringTie into read count tables (at gene and transcript levels) which can be then imported into packages like DESeq2 or edgeR in order to estimate differential expression for genes and transcripts. Please check the new manual section for this DESeq2 and edgeR integration.

I bet they were talking about this script

See also

Answer 1

[Kristoffer Vitting-Seerup]

I highly recommend using tximport to import the data due to all the reasons outlined in the Bioconductor workflow Analyzing RNA-seq data with DESeq2.

To use tximport with StringTie data you simply need to make a vector with the paths to each of the "t_data.ctab" files:

quantData <- c(
    'path/to/sample_1/t_data.ctab',
    'path/to/sample_2/t_data.ctab'
    ...
)


 tximport(
     files = quantData,
     ...
 )

[ankur]

I could import my data successfully. Thank you kristoffer.vittingseerup

[Kristoffer Vitting-Seerup]

Then remember to accept the answer :-)