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Forum: Metagenomics

09-23-2012, 03:05 AM

Replies: 3

Tool to identify 16s rRNA fragments in raw data

Views: 3,843

Posted By faozhi

or EMIRGE? https://github.com/csmiller/EMIRGE

or EMIRGE? https://github.com/csmiller/EMIRGE

Forum: Illumina/Solexa

04-05-2012, 05:36 AM

Replies: 5

How to count aligned RNA-seq reads after sequenced and aligned by Illumina?

Views: 3,040

Posted By faozhi

You have to map the reads to the reference...

You have to map the reads to the reference genome. To count, you might want to try cufflinks.

Forum: Metagenomics

04-04-2012, 10:09 PM

Replies: 12

Illumina Metagenomics data

Views: 6,071

Posted By faozhi

I would trim the reads (based on qual and remove...

I would trim the reads (based on qual and remove adapters), then start assembling.
If you would like to know who are there, you could use MG-RAST or just blastn your trimmed reads against greengenes...

Forum: Bioinformatics

04-04-2012, 10:03 PM

Replies: 5

Pre processing of Illumina data

Views: 2,385

Posted By faozhi

I know I didn't combine them during trimming...

I know I didn't combine them during trimming based on qual...

Forum: RNA Sequencing

12-05-2011, 11:04 PM

Replies: 0

Calculate transcript abundance for prokaryotes

Views: 1,571

Posted By faozhi

Calculate transcript abundance for prokaryotes

post deleted

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