06 June 2014 5 4K Report

We are planning a metatranscriptomic analysis on a microbial community obtained from bioreactors, but we need to remove as much rRNA as possible in order to maximize the number of reads on mRNA. We have found in literature some kits developed to remove the rRNA but we would have some suggestions from people that have tested rRNA depletion kits.

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Are you looking for a position as postdoc or other in bioinformatics about microbial genomics or metabolic flux balance?

We are hiring! Are you a postdoc or did you just graduate? Would you like to work on metabolics flux balance or microbial genomics for anaerobic digestion topic? Then contact us! We are looking...

07 August 2019 1,917 3 View

Can someone suggest a good textbook or other online material for metagenomics?

Next year I will start teaching metagenomics to master students (mainly focused on bioinformatics). Can anyone recommend a text book related to this topic? I am also interested in other related...

05 June 2019 1,370 16 View

How to delete a gene in Lactobacillus paracasei?

Hi, I would like to perform gene disruption in Lactobacillus paracasei. Could you provide a protocol or suggest a grup which is able to perform this kind of analysis? Thank you

07 August 2018 4,356 1 View

Is it possible to perform hierarchical clustering of a very large number of features?

I am checking different methods to perform hierarchical clustering with a very large number of elements (between 100,000 and 500,000). I have tried many different software like MeV, Cluster, etc....

10 November 2015 7,580 4 View

Can anyone suggest a software to compare microbial genome characteristics?

I am comparing a large number of microbial genomes obtained from a complex microbial community. I performed the main functional annotations for the genes (COG, KEGG, Pfam) and I would perform a...

01 February 2015 9,918 1 View

Has anyone obtained worse assembly results using metavelvet than using velvet?

We are performing trial shotgun assemblies of 80 millions paired-end sequences illumina reads obtained from a bioreactor microbial community. After removing contigs shorter than 1kbp, the assembly...

03 April 2014 7,391 1 View

Can someone suggest primers for 16S rDNA genes matching both Archea and Bacteria?

I am planning analysis on a complex microbial community containing high number of species of bacteria and archaea using 16 rDNA sequencing. On previous experiments I have used two different...

01 February 2014 8,774 8 View

Bowtie and bwa, problems with very large databases - can anyone help?

I am trying to align short reads DNA sequences on a reference database comprising all the prokaryotic genomes reported at the ncbi. Unfortunately I noticed that both BOWTIE and BWA have a maximum...

11 December 2013 4,517 4 View

Assembly of metagenomics shotgun sequences obtained with the Proton sequencer

Does someone have assembled short reads obtained from shotgun sequencing (Proton sequencer) of complex microbial communities? Which is the best tool for assembly of these reads (not-paired-end)?...

08 September 2013 6,967 4 View

Which is the best tool for operon prediction in bacteria?

I am analyzing a bacterial genome recently sequenced in our group. After gene finding and annotation I would have a rough overview of its operon structure using a bioinformatic software. Can...

08 September 2013 3,518 1 View

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