Question: Is bowtie adopting AI to become smarter !! :P
0
gravatar for Prasad
18 months ago by
Prasad1.6k
India
Prasad1.6k wrote:

Hi all,

I have come across very peculiar alignment results for plant RNASeq data. I have aligned RNASeq data 150 *2 illumina stranded library [think matters only during expression quantification]. Aligned to its reference genome (https://www.ncbi.nlm.nih.gov/assembly/GCA_000826755.1) using bowtie2, tophat2, hisat2 and STAR (all run with default parameters. Same parameters of bowtie2 were used in tophat and hisat). It was interesting to see bowtie out performs splice aware aligner (expect STAR which wins marginally). Here are the stats (%),

Bowtie2- 53.57

tophat2 - 12.5

hisat2 - 39.24

STAR - 58.64

Similar post were there 1, 2 and could not find a conclusive result. From unaligned reads, 5 random set of 100 reads were checked, 60% of the sequences found match in blast result of which 72.09 are still matching to predicted mRNAs of the reference genome.

My questions, 1) Star being local aligner, how come these reads are missed out? (is it because long exon-exon junction gap)

2) How bowtie is performing better than splice aware programs?

rna-seq alignment • 665 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by Prasad1.6k
3

Better? I'll write an aligner which will align 100% of the reads for you, but with a very low accuracy.

Is bowtie adopting AI to become smarter !!

Nope.

ADD REPLYlink modified 18 months ago • written 18 months ago by WouterDeCoster39k

I was just curious to know how bowtie performed better than splice aware aligners. header i meant in fun way

ADD REPLYlink modified 18 months ago • written 18 months ago by Prasad1.6k

Sure, but the percentage aligned doesn't make it better, since it doesn't say anything about how correct the reads are. Perhaps Bowtie aligns to one exon only, and splice information is completely lost?

ADD REPLYlink written 18 months ago by WouterDeCoster39k

As per Wouter, the % alignment is not the complete story. You have neither given us data for BWA (even though I would use neither Bowtie2 nor BWA on their own for RNA-seq reads).

ADD REPLYlink written 18 months ago by Kevin Blighe43k
1

True. I wanted to have quick view on the data so choose bowtie, when % was only 53 then i went for splice aligners (tophat and hisat) those results were much lesser (was expecting it to be better than bowtie). When i checked unaligned, they are still matching to jujube. is it the data which is a questionable?? Here unaligned reads from star.

Thank you WouterDeCoster and Kevin Blighe for your valuable suggestions

ADD REPLYlink written 18 months ago by Prasad1.6k
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