Question

bowtie, tophat vs BLAST

1

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9.5 years ago

niu2rseq ▴ 90

Hi,

I have a very basic question but it confused me a little bit.

For a metatranscriptome data, we can compare it with the NCBI prokaryote genome collections. Shall I use bowtie, tophat these kinds of mapping tools here, or just use BLAST here? What's the difference between this two kinds of tools? What kind of different downstream analysis would be available only for one tool?

Thanks!

BLAST RNA-seq tophat bowtie metatranscriptome • 6.4k views

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by niu2rseq ▴ 90

Ram · Answer 1 · 2014-10-31

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9.5 years ago

Ram 43k

Hi,

TopHat and Bowtie are aligners - they align short sequences, typically reads, to reference genomes. You are comparing a metatranscriptome to a genome. BLAST should be better suited for you.

ADD COMMENT • link 2.2 years ago by Ram 43k

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Thank you RamRS.

So shall I perform some kind of assembly of the metatranscriptome reads before doing the BLAST? Can BLAST give me also the expression profiles of each detected bacterial genes?

Thanks!

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by niu2rseq ▴ 90

1

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If you have contigs, you will be able to detect more gene sequences, since the contigs are bigger than reads. If you want to do gene prediction, I will vote for doing a little assembly first.

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by iraun 6.2k

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Hi, I really like your idea!

So if we want to get the expression profile of each microbial genes to see the dynamics, shall we use bowtie/tophat plus cufflinks, or we can use BLAST tools for this purpose?

ADD REPLY • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by niu2rseq ▴ 90