Question: bowtie problem: cannot locate bowtie index
gravatar for biolab
5.7 years ago by
biolab1.2k wrote:

Hi everyone,

I actually have three minor questions about bowtie.  I wrote a file as follows:

bowtie2-build rrna.fa rRNA
bowtie2 --very-sensitive  -x rRNA  -f reads.fa --un a.fa
bowtie2-build genome.fa GENO
bowtie2 --very-sensitive  -x GENO  -f a.fa  --un b.fa

However, when running bash, I was encountered a problem as follows.  This is my first question.

Could not locate a Bowtie index corresponding to basename "GENO"
Error: Encountered internal Bowtie 2 exception (#1)

My second question is related to bowtie --very-sensitive option.  Does this option map more reads on the genome?

My third question is about bowtie vs tophat. My understanding is: bowtie can not detect exon splicing, so abandoned  some mapping reads; in contrast, Tophat overcomes this problem and enables more reads  mapping on genome.  Is my understanding right?

THANK YOU very much!

bowtie • 6.9k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 5.7 years ago by biolab1.2k
gravatar for Devon Ryan
5.7 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:
  1. Presumably something was mistyped in the bowtie2-build command when you tried to build the GENO index. Just look and see what files are in that directory and how big they are. In practice, it's simplest to just run the bowtie2-build command yourself and ensure that it doesn't throw an error message.
  2. Not necessarily. I've had it map fewer with that option, though the difference is quite small. The --very-sensitive and --very-sensitive-local presets mostly affect reads that can align with a high edit distance. However, since the seed size changes with these, you may occasionally exhaust the number of seed extensions before finding the actual best alignment (this is true with any setting, but is more likely to occur as the seed size is decreased). Having said that, you'll typically get a few more reads mapped with these settings, though it'll take longer to do so.
  3. Correct, bowtie2 isn't intended to map mRNA to the genome and will miss splice junctions. If you have that sort of data and sufficient RAM, then use STAR instead. It's MUCH faster than tophat2 and produces equally good results.
ADD COMMENTlink written 5.7 years ago by Devon Ryan96k

Hi Devon,

Thank you very much for your detailed explanations, all of which are helpful for my work.

ADD REPLYlink written 5.7 years ago by biolab1.2k

I'm accepting this answer so Biostars bot doesn't bump it again.

ADD REPLYlink written 2.4 years ago by RamRS30k
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