Connecting DESeq2 Expression values to BLAST gene ID output

Question

[awhite66751]

To give an outline of my process so far, I have used DESeq2 on my fq sample files against a trinity de novo assembly to get differential expression values. This gave me a file w/ the gene ids as the Trinity transcript IDs. I then pulled only the Trinity IDs w/ a p-adjusted <0.01 out of the original assembly and ran those in BLAST to ID the significant deferentially expressed genes. My problem is connecting these two sets of data together so I have the expression values together with the gene ID so I can do further downstream analysis.

[lieven.sterck]

what have you tried so far to accomplish this? and what 'environment' are you working in, windows, unix, R, ... ?

Answer 1

[swbarnes2]

If you are looking for a pre-packaged thing to do this, I don't think it exists. I think you are going to have to make something yourself.

Answer 2

[lieven.sterck]

Not a 100% sure I fully get your input but assuming you have two tabular files with each 2 columns. One file with trinityID - expr value and ones file with trinityID - blastID , then perhaps this linux oneliner might help :

sdiff <trinity file> <blast file> |grep '|' | awk '{ print $5,$1,$2 }'

this will compare both files, grep the common lines, print out to a new file a 3-column list with blastID-trinityID-expr value (space delineated)

make sure you have both file sorted on the first column though