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Thread | Thread Starter | Forum | Replies | Last Post |
Metagenomics/Metatrancriptomics Sequencing | newBioinfo | Core Facilities | 11 | 09-20-2013 11:41 AM |
Metagenomics/Metatrancriptomics Sequencing | newBioinfo | Metagenomics | 0 | 09-13-2013 10:51 AM |
16s rRNA gene sequencing(metagenomics) | newBioinfo | Sample Prep / Library Generation | 0 | 03-26-2012 05:08 PM |
16s rRNA gene sequencing(metagenomics) | newBioinfo | Illumina/Solexa | 0 | 03-26-2012 02:24 PM |
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#1 |
Member
Location: MO, USA Join Date: Apr 2011
Posts: 82
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Hi,
I just started my first metagenomics shot-gun sequencing analysis. I hope I can get some advice here. 1. QC process: I am looking at removing duplicate sequences and trimming low quality bases, according to this HMP's SOP. Is this adequate? What is considered a good QC practice? 2. Data analysis: I am first trying MetaPhlAn by Huttenhower's group. Is there any 'standard' procedure/workflow that this community recommends? Thanks for your help, John |
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#2 | ||
Senior Member
Location: California Join Date: Jul 2014
Posts: 197
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Quote:
We've just gotten into shotgun too, so happy to share any advice. |
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#3 | |
Member
Location: MO, USA Join Date: Apr 2011
Posts: 82
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Thank you very much for your reply. At this point, any thing will help me get started.
![]() have a nice weekend, John Quote:
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#4 |
Member
Location: Germany/Netherlands Join Date: Feb 2014
Posts: 98
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Other things you'll need to do:
- assembly, best cross-assembly if you have multiple samples - genomic binning (e.g. maxBin) - gene prediction (prodigal has a setting for meta, but only bacteria; ncRNAs can be predicted with rnammer, trnascan-SE and rfam) - function prediction (via KO, InterproScan, PRIAM, dbCAN, etc) |
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