best RNAseq mapping tool for bacteria

sissi · 03-04-2012, 07:10 PM

Hi,

I am new to NGS data and am trying to find the best mapping tool for bacterial genome. My data consists of FASTQ files for paired end RNA-seq on Illumina. I have downloaded the reference genome from NCBI website (fasta file).
So far I have identified a few softwares (MAQ, Tophat, BWA, Glimmer, SHRIMP...), but I don't know which one to choose.

Thank you for your help!

Regards,
S

swbarnes2 · 03-05-2012, 12:07 AM

Bacteria have almost no introns, so you are just mapping to the genome. And since the genome is so small, you can use as slow an algorithm as you like, it'll still be done pretty fast.

As long as it'll output .bam files, you'll probably be fine.

swaraj · 03-05-2012, 04:33 AM

For aligning RNA-seq reads consider the following points

1) Paired-end or single-end sequencing?
2) spliced reads?
4) interested in finding novel transcripts?

I suggest subread (http://subread.sourceforge.net/) as it is fast, reported to be accurate and integrates within R environment.

sissi · 03-05-2012, 05:55 AM

Hi,
Thx for your answers.

It is for pair end sequencing data with 75bp library.
I will be looking at SNPs and differential expression data.
I don't know exactly if there are many spliced read, but my guess would be very little as it's a bacteria.

I read a few papers on the subject and it seems that the quality of the reference genome is also important. How do I know if that condition is verified?

I will have a look at the R script

Thank you!

Hobbe · 03-05-2012, 06:01 AM

Shrimp2 is easy to use and runs very well on several cores if you have them, so it is fairly quick. In my experience, it maps well too.

swaraj · 03-05-2012, 06:16 AM

Shrimp2 is a good choice for bacterial genomes. For the genome quality you have to look into the publication which reported the genome.

sissi · 03-05-2012, 04:48 PM

Thanks a lot.

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03-04-2012, 07:10 PM	#1
sissi Junior Member Location: Singapore Join Date: Mar 2012 Posts: 5	best RNAseq mapping tool for bacteria Hi, I am new to NGS data and am trying to find the best mapping tool for bacterial genome. My data consists of FASTQ files for paired end RNA-seq on Illumina. I have downloaded the reference genome from NCBI website (fasta file). So far I have identified a few softwares (MAQ, Tophat, BWA, Glimmer, SHRIMP...), but I don't know which one to choose. Thank you for your help! Regards, S

03-05-2012, 05:55 AM	#4
sissi Junior Member Location: Singapore Join Date: Mar 2012 Posts: 5	Hi, Thx for your answers. It is for pair end sequencing data with 75bp library. I will be looking at SNPs and differential expression data. I don't know exactly if there are many spliced read, but my guess would be very little as it's a bacteria. I read a few papers on the subject and it seems that the quality of the reference genome is also important. How do I know if that condition is verified? I will have a look at the R script Thank you! Last edited by sissi; 03-05-2012 at 05:58 AM.

03-05-2012, 12:07 AM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	Bacteria have almost no introns, so you are just mapping to the genome. And since the genome is so small, you can use as slow an algorithm as you like, it'll still be done pretty fast. As long as it'll output .bam files, you'll probably be fine.

03-05-2012, 04:33 AM	#3
swaraj Member Location: Naples, Italy Join Date: Feb 2012 Posts: 50	For aligning RNA-seq reads consider the following points 1) Paired-end or single-end sequencing? 2) spliced reads? 4) interested in finding novel transcripts? I suggest subread (http://subread.sourceforge.net/) as it is fast, reported to be accurate and integrates within R environment.

03-05-2012, 06:01 AM	#5
Hobbe Member Location: Uppsala, Sweden Join Date: Apr 2010 Posts: 29	Shrimp2 is easy to use and runs very well on several cores if you have them, so it is fairly quick. In my experience, it maps well too.

03-05-2012, 06:16 AM	#6
swaraj Member Location: Naples, Italy Join Date: Feb 2012 Posts: 50	Shrimp2 is a good choice for bacterial genomes. For the genome quality you have to look into the publication which reported the genome.

03-05-2012, 04:48 PM	#7
sissi Junior Member Location: Singapore Join Date: Mar 2012 Posts: 5	Thanks a lot.