NGS data analysis

Question

[CancerGuy]

I have three different excel files from three biological replicates with fold change values (transcriptome analysis). I want to combine all the data in one file, but the problem is the sequence of gene listing in file is different in all three files (eg. gene A is on 1st place in first file but is on 157th and 3045th place in file 2 and 3, respectively). This makes simple copy-paste impossible. Is there any other way to arrange this data? Thanks in advance.

[GenoMax]

Are those columns sorted by the fold change values? Should it not be simple enough to re-sort the data using the gene name column and then combine the data columns in a new file/workbook?

[CancerGuy]

Some genes are missing in one or other file (due to zero read, i guess), and i have whole transcriptome there. Even after arranging gene name column i found data was not aligned correctly.

[GenoMax]

You may be able to use join (https://unix.stackexchange.com/questions/102298/join-two-files-with-different-number-of-columns-and-rows), VLOOKUP in excel or do this in R.

[Jake Warner]

Join is good. Merge() in R also works quite well for this kind of thing:

 merge(x, y, by.x='gene' by.y = 'gene', all =T)

[CancerGuy]

I'll try your suggestions. Cheers.

[mbk0asis]

'vlookup' in MS Excel might work for you.

Answer 1

[AB]

You can use dplyr and join them.

If you want to retain all the rows in both datasets, use full join

full_join(x,y,by=c('gene.x'='gene.y')

You can use inner_join, left_join or right_join depending on whatver you want.

[CancerGuy]

Awesome! That's what I was looking for.