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I am using a platform "Bcbio" for processing RNASeq fastqs. At the end of the process, it generates a number of files like counttables, sailfish raw data and so on. There is also a file called "combined.dexseq" which looks like;

id  Control_rep1_1  Control_rep1_2  50ng_1  50ng_2  250ng_1 250ng_2
ENSG00000000003:001 458 495 688 643 619 622
ENSG00000000003:002 143 140 204 153 166 163
ENSG00000000003:003 93  65  117 101 80  112
ENSG00000000003:004 50  47  68  73  54  89
ENSG00000000003:005 66  62  85  109 71  104
ENSG00000000003:006 97  93  152 163 131 153

I want to run a DEXSeq analysis following the vignette but the problem is vignette generates the data form that I have at the very end when featureCounts() function is used.

Can anyone help me with estimating exon fold changes and using other important functions for analysis with using the file format that I have?

zx8754
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Fırat Uyulur
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  • Given the information you provide it's difficult to deduce what you've done so far. Your "combined.dexseq" is your count file, with counts per exon per sample. You will need the matching flattened gff annotation file, a `dataframe` with the sample definition, and a design formula to set up the GLM. Have a look at section "Preparing the annotation" from the document you link. It explains how to create the flattened annotation file. – Maurits Evers Oct 25 '16 at 22:54

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