Research paper (p.564, 2nd paragraph: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html) told me that Bowtie will align RNA segment with reference genome. TopHat too but TopHat can break up the sequence which isnot identified into small piece to align with reference genome and It's suitable for mapping spliced RNA (eukaryote) but some introns were identified in bacteria
Is it ok to align "bacterial" transcriptome with reference genome by "TopHat"
In my opinion, TopHat might need more depth to match exon
I will appreciate your suggestion
thank you in advance
Chooseel (newbie in RNA-seq)
So, the results of both software are very similar for bacterial transcriptome?
I am very new in this field of research. please explain more
thank you very much
I am not quite sure about the bowtie output, but one advantage of running TopHat is that you can easily run your results through the rest of the TopHat pipeline. Like annotation, gene expression analysis, and differential gene expression calculation. When you run TopHat you can omit the splicing/read segmentation step to make it like bowtie.
I concur with Rohan and would like to add that if your % mapping read is high in case of bowtie1 than nothing to worry about it but if your read mapping % is low than you can also use BWA or bowtie2 (with gap alignment feature).
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