Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
metatranscriptome mapping Francy87 Bioinformatics 2 09-24-2013 08:08 PM
best RNAseq mapping tool for bacteria sissi Bioinformatics 6 03-05-2012 03:48 PM
PubMed: Optical mapping of DNA: Single-molecule-based methods for mapping genomes. Newsbot! Literature Watch 0 01-06-2011 02:00 AM
De-novo assembly of bacteria genomes - which tools? maasha Bioinformatics 8 08-12-2009 01:41 PM

Thread Tools
Old 10-28-2014, 01:04 PM   #1
Location: Italy

Join Date: May 2013
Posts: 28
Question mapping bacteria metatranscriptome to genomes

Hello! I'm pretty new to rna-seq data analysis and I'm not sure about how proceed with it.
I have bacteria metatranscriptome reads from environmental samples and I know more or less which species are present. So I'd like to try to map them to some genomes (those of the species I know that should be there), using bowtie. I don't know about where to find the genomes and which file formats I need. I'm wandering about downloading them from here, but for each genome there are a lot of different files. As I could understand, I need .ffn to build the bowtie index (if I want to use only the protein coding parts of the genomes). But then, in which file do I find the corresponding gene annotations (so the names of the genes)?

Francy87 is offline   Reply With Quote

bacteria, bowtie2, mapping, metatranscriptome, rna-seq advice

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 06:04 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO