sorting columns by same values to do DEG analysis

Question

[dllopezr]

Hi community!

I am working with metagenomic output from MG-RAST, but the columns don't match and I need to solve this before doing my DeSEQ analysis. The table is something like this

GeneName Count GeneName Count GeneName Count GeneName Count
GeneA       x  GeneB      x   GeneA    x     GeneA     x

The Genes could be present for all, three, two or only one treatment. I need a way to sorting the columms to match by gene name.

Do you know any way to do this in r or excel?

Thank you so much!

[k.kathirvel93]

All genes present in all samples ? means the number of genes is same in all samples? If yes, then go for an A-Z or Z-A sorting.

[finswimmer]

Hello,

I don't understand the criteria for your sorting. But the standard tool for sorting text file is sort

fin swimmer

Answer 1

[Fabio Marroni]

Looks like you have a file that derives from merging the genes observed in 4 samples.

In R: split the four sets (column 1-2, column 3-4, column 5-6, column 7-8) and then use the merge command to merge by gene name.

In Excel: merge the 4 lists carrying the genes and remove duplicates (so that you have all the genes observed, and only once), and then you can either use the vlookup function or build a pivot table.