MG-RAST file upload

[morning latte]

Hello,

I am uploading fastq files and wondering if they should be interleaved format or separate format (R1 and R2). I am not able to use the function of ""join paired-ends" of MG-RAST as I already QC'd reads and the number of reads in each R1 and R2 files do not match. If the files should be interleaved format, should I upload orphans too? Thanks.

[fibar]

Hi,
This is an old thread, but I'll answer anyway because I'm working on these things. In my opinion:
1st) It's recommended to upload fastq raw data to MG-RAST. That standarizes the procedure and the end results, and allows other people to compare data sets later.
2nd) Join paired-ends, according to the manual, says sequences must have overlap. Do they overlap? If not, as my case, either upload:
a) R1 and R2 files separately
b) R1 and R2 files concatenated in a same file (I haven't done this but it should be OK)
c) assembly and then upload contigs only
d) assembly and then upload contigs and orphans

I'd like to see some reply on this. All the best.