CummeRBund wiothout annotaation

[nr23]

Hi guys,

I'm trying to get a list of differentially expressed genes using cummerbund - which is working well using this sort of thing:

cuff_data <- readCufflinks('diff_out')

diffGeneIDs <- getSig(cuff_data,level="genes",alpha=0.01)

length(diffGeneIDs)

I can see that I have 342 genes sig DE (P<0.01) genes between the groups, and I can see there IDs.

However, as I don't have a annotation track, what I really want to be able to do from here is to essentially BLAST these genes to find out what they are.

Is there any way of pulling out nucleotide sequence using cummeRbund?

Many thanks

[AgaricX]

If you check the gene_exp.diff file from CuffDiff and use the XLOC name, you can get the chromosome and coordinates for each locus. From there, you can use SAMtools view to pull out all the reads from your BAMs in that region and assemble those to use as your BLAST query.

Good Luck!

[nr23]

Thanks - I have had success doing something similar (using grep "XLOCs" within the gene_exp.diff file and finding and blasting the corresponding region -(I've aligned to a cds file rather than genome)).

However, this must be a problem a lot of people working without annotation tracks encounter - so I'm hoping I'll be able to find a pipeline for this, as it will be very time consuming to do this for every over expressed gene for lots of conditions.

Best,

N