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Old 12-22-2017, 05:46 AM   #1
stevebaeyen
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Default de novo metatranscriptomics pipeline for soil

Hi all, I'm trying to figure out a good pipeline for a de novo metatranscriptomics project on soil and rhizosphere samples. I'm looking into the Khmer protocols which use Trinity, but I wonder if there are other good pipelines or scripts around for this purpose. Any advice is welcome !
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Old 01-03-2018, 01:55 AM   #2
stevebaeyen
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Default de novo metatranscriptomics

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Originally Posted by stevebaeyen View Post
Hi all, I'm trying to figure out a good pipeline for a de novo metatranscriptomics project on soil and rhizosphere samples. I'm looking into the Khmer protocols which use Trinity, but I wonder if there are other good pipelines or scripts around for this purpose. Any advice is welcome !
Nobody willing to share advice on this subject?
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Old 01-03-2018, 02:24 AM   #3
Gorgon_VZ
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Default

Hi, I just found a list of tools on this webpage (http://www.metagenomics.wiki/pdf/def...ranscriptomics). Personally I only used Kraken so far, but actually Kraken only assigns taxonomic units to reads and not functional or genexpression stuff like rpkm. But maybe one of the other tools might be of some interest.

Kallisto - RNA-seq transcript abundance estimation
Kraken - assigns taxonomic labels to short sequencing reads
HUMAnN2 - community-wide gene transcription and pathway analysis
requires pairs of DNA and RNA sequencing of the same biological sample
PanPhlAn - strain-specific transcriptomics analysis
requires pairs of DNA and RNA sequencing of the same biological sample

Maybe it could also be worth to have a look at MetaTrans, MEGAN,COMAN or SAMSA.
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