Question: Importing kallisto's abundance files into DESeq2 pipeline
0
gravatar for deena
2.1 years ago by
deena10
Germany
deena10 wrote:

Hi,

I am glad that tximport is introduced with option to import counts from kallisto, RSEM etc. I have 6 RNA-seq samples. I have quantified every sample using kallisto. For every sample, abundance.tsv file and abundance.h5 files were generated. Now in order to make use of kallisto abundance_estimation,

1) Should I take only the estimated counts column from each sample and make a data frame which is later imported In DESeq2 pipelne

2) Should I convert every abundance.tsv(or abundance.h5) file using tximport ? How to combine every sample's abundance.h5 file?

Kindly gudie me

Thanks in advance

                

deseq2 kallisto • 385 views
ADD COMMENTlink modified 2.1 years ago by Michael Love25k • written 2.1 years ago by deena10
Answer: Importing kallisto's abundance files into DESeq2 pipeline
0
gravatar for Michael Love
2.1 years ago by
Michael Love25k
United States
Michael Love25k wrote:

Can you take a look at the tximport vignette for the recommended function calls? We have example code specific to the different methods.

ADD COMMENTlink written 2.1 years ago by Michael Love25k
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