I am trying to analyze Ribo-seq data on Zea mays and have already mapped my files using Bowtie2 and have used this for my most recent analyses. I have come across another way to analyze ribosome profiling called riboSeqR and it requires the sequences to be mapped with Bowtie, not Bowtie2. I was wondering why they would require that? I don't want to have to remap all of my sequences if it turns out Bowtie is outdated.
Thanks for your help!
Bowtie is for relatively short reads up to 50 bp. If your reads are more then 50bp better to go with Bowtie2. In Bowtie 2 gaps and gap lengths are not restricted. whereas bowtie finds only ungapped alignments. So if your ribosomes reads less than 50bp then you can use riboseqR. And if it is more than 50bp better to use Bowtie2.
Bowtie is for relatively short reads up to 50 bp. If your reads are more then 50bp better to go with Bowtie2. In Bowtie 2 gaps and gap lengths are not restricted. whereas bowtie finds only ungapped alignments. So if your ribosomes reads less than 50bp then you can use riboseqR. And if it is more than 50bp better to use Bowtie2.
ribo-seq data length would be varied between 26bp - 36bp, and 30bp or 31 bp is the main distribution. As @Anuraj Nayarisseri and @Mathew A Beale have mentioned that bowtie2 is designed for longer reads, bowtie is designed for shorter reads (in bowtie paper, they've aligned reads over 50bp but has worse performance)
the format ouf sam output will be the same from both tools, but the speed and accuracy are different. bowite has better accuracy and speed over bowtie2. And for any case, if you would realign your data use bowtie, use bowtie -v (more accurate than -n)
https://www.dropbox.com/s/fkr4nlj5kv7kojs/Figure1.png?dl=0
(30bp reads simulated reads, aligned to human transcriptome, sam results validated by checking the sequence coordinate of where they sampled from and where they have aligned to, and compare the sequence distance of query sequence and aligned sequence )
i just want to give some hints on the aligner's performance.
I am really sorry, but since when does bowtie1 perform better then bowtie2? Also I dont get the figure that you show. Bowtie1 is faster which is shown. However, it does not show difference in the mapping plus it does not show mappings with more then 1 SNP.
I would always use bowtie2 over bowtie since it is more robust against snps and sequencing errors.
@Priscilla Glenn Have you tried running it with the output of Bowtie2. It can be that they used bowtie1 back then and did not bother to update the requirements.
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