Importing kallisto's abundance files into DESeq2 pipeline
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deena ▴ 20
@deena-7415
Last seen 5.0 years ago
Germany

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 • 809 views
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@mikelove
Last seen 2 hours ago
United States

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

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