Deseq2 Error: Differnt number of rows in featureCount files

[Aditi_Sharma]

So, I had two datasets A and B, and featureCount files for each. When I use these files as input in deseq2, it gives me the error:
Error in data.frame(…, check.names = FALSE) :
arguments imply differing number of rows: 4659, 4644
Calls: get_deseq_dataset … eval → eval → eval → cbind → cbind → data.frame

I understand that the total number of rows in each featureCount file is different, how do I overcome this?

[Nadra]

Hi Aditi,
Wondering if you were able to overcome this problem, I have the same issue and not sure what to do.

[jennaj]

@Aditi_Sharma

I understand that the total number of rows in each featureCount file is different, how do I overcome this?

@Nadra

I have the same issue and not sure what to do.

Hi @Nadra

The number of rows in the input count files should be identical. Did you use the same reference annotation for each? The built-in annotation will also produce that.

You want one row for every gene feature for most use cases.

Check that first and let us know.