Hi,
I have a few general questions how to analyze metagenomes.
Platform: Illuminia Highseq, 2x 150 bp PE reads with ~80 bp overlap
Aim: Get taxonomic representation and functional profile (e.g. KEGG)
Preferred tool: MEGAN 5
My questions to get started:
1. Should I first merge the paired reads by their overlap or should both be analyzed seperately? In MEGAN I could check a box for PE reads, so maybe not merging them serves a purpose. If I should merge, which tool do you recommend?
2. Should I collapse my sequences before blasting them. I could do that to group identical reads to OTUs. They get a new header than, stating how often that OTU was present. That would greatly reduce the blast time. Question is, can downstream tools like MEGAN deal with that?
3. Any recommended BLAST settings to get a good balance between accuracy and computational time?
Sorry for these stupid questions. I am not a bioinformatician. I am normally a try and error learner. But if every computational step takes several days, I better go the right way from the start...
Thanks,
Sören
I have a few general questions how to analyze metagenomes.
Platform: Illuminia Highseq, 2x 150 bp PE reads with ~80 bp overlap
Aim: Get taxonomic representation and functional profile (e.g. KEGG)
Preferred tool: MEGAN 5
My questions to get started:
1. Should I first merge the paired reads by their overlap or should both be analyzed seperately? In MEGAN I could check a box for PE reads, so maybe not merging them serves a purpose. If I should merge, which tool do you recommend?
2. Should I collapse my sequences before blasting them. I could do that to group identical reads to OTUs. They get a new header than, stating how often that OTU was present. That would greatly reduce the blast time. Question is, can downstream tools like MEGAN deal with that?
3. Any recommended BLAST settings to get a good balance between accuracy and computational time?
Sorry for these stupid questions. I am not a bioinformatician. I am normally a try and error learner. But if every computational step takes several days, I better go the right way from the start...
Thanks,
Sören
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