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Hello, Seqanswers community!
I am going to ask a very newbie question now, please bear with me...
I am analysing some metagenomic data (tick guts - shotgun sequence on Illumina - read length: 101).
At the moment my target is to determine "who's there" and gene identification.
I am planning to use Megan 4.0 and MG Rast to start with, but I had a look at several reviews and algorithms and there are some parts of the general analysis workflow which I am not sure I understand.
When using algorithms like Frag Gene Scan, as an example, their output is a list of reads which are presumably part of genes. How do I use this output then? Do I BLAST it against databases like NCBInr?
A similar doubt with Metacluster 5. It cluster reads, but being an unsupervised algorithm, there is no taxonomic assignment. What would be the next step in this case?
Thanks for your patience.
Also, here are some of the reviews I found useful, in case some other novice is interested:
Regards,
Max
I am going to ask a very newbie question now, please bear with me...
I am analysing some metagenomic data (tick guts - shotgun sequence on Illumina - read length: 101).
At the moment my target is to determine "who's there" and gene identification.
I am planning to use Megan 4.0 and MG Rast to start with, but I had a look at several reviews and algorithms and there are some parts of the general analysis workflow which I am not sure I understand.
When using algorithms like Frag Gene Scan, as an example, their output is a list of reads which are presumably part of genes. How do I use this output then? Do I BLAST it against databases like NCBInr?
A similar doubt with Metacluster 5. It cluster reads, but being an unsupervised algorithm, there is no taxonomic assignment. What would be the next step in this case?
Thanks for your patience.
Also, here are some of the reviews I found useful, in case some other novice is interested:
Regards,
Max