Exporting functional data with sample information



I have been struggling to find how to export functional data with sample information. Each sample is a separate sam file which I loaded into the Import from Blast dialogue box altogether. I then uploaded the SEED reference database and ran the alignment. My rma output seems to merge all the samples together though, so I effectively have one large pooled sample. Is there a way to export functional information so that I can analyse the data on a per sample basis?

Many thanks,



I do this in the ‘Compare’ view, loading in all the files and then exporting the data to a CSV.


Hi Chris, thanks for your reply. Unfortunately my problem is that I have only one rma6 output file after loading multiple sam files into the Import from Blast box and aligning in MEGAN, so I cannot use compare view to look at different samples. I think sample ID information must have been retained in this output file, but I don’t know how/if it is possible to extract it.


Please let me know whether MEGAN perform functional annotation for paired end data.


You need to import each file separately, not all together at the same time. Then each SAM file will give rise to a different RMA file and you can then open the RMA files together using the Compare dialog.