[doxologist]

quick question: I heard anecdotal reports that bowtie misses a large number of matches compare to programs like Maq. have anyone else heard this? in terms of %, does anyone have any numbers?

[Ben Langmead]

Hi Doxologist,

The circumstances under which Bowtie might miss alignments that are "valid" according to its alignment policy are outlined in the manual (see last paragraph of section "Maq-like Policy"). These misses only occur in -n 2 and -n 3 modes, and they can be avoided by increasing the --maxbts parameter (at the cost of some speed). Unless your read data is very low quality, the fraction of reads missed due to the backtracking limit in -n 2 mode is generally very small (<1%).

Note that when you run 'maq' with -n 2 option (the default), it will find some alignments that actually have 3 mismatches in the seed. Bowtie will *not* report alignments with 3 mismatches in the seed unless -n 3 is specified. It's likely that this is the source of the difference that the anecdotal reports are referring to.

Thanks,
Ben

[doxologist]

thanks... that's helpful.

any thoughts on bwa and SOAP2?

[Ben Langmead]

I haven't spent much time looking at BWA and SOAP2, so I'm not the expert. I like Bowtie :-), but I know others who use and are happy with BWA. I haven't met anyone with much experience with SOAP2. There is a post earlier in this thread by Heng Li that talks a little about the key differences among the three. I heard that Heng Li also has some benchmarking results that he's made public somewhere...

Thanks,
Ben

[doxologist]

thanks for the response.

here's the link to the comparison Heng Li did...

http://maq.sourceforge.net/bwa-man.shtml

[danielsbrewer]

Does anyone know whether bowtie supports aligning multiple read lengths?

I am doing small RNA Solexa sequencing and so after the adapter has been removed I end up with variable length reads. With MAQ it appears that you have to run it multiple times for the different lengths, is bowtie the same?

[ewingad]

Does anyone know whether bowtie supports aligning multiple read lengths?

I am doing small RNA Solexa sequencing and so after the adapter has been removed I end up with variable length reads. With MAQ it appears that you have to run it multiple times for the different lengths, is bowtie the same?

Yes it does!

-Adam

[doxologist]

Does anyone know whether bowtie supports aligning multiple read lengths?

I am doing small RNA Solexa sequencing and so after the adapter has been removed I end up with variable length reads. With MAQ it appears that you have to run it multiple times for the different lengths, is bowtie the same?

we had a similar discussion in another thread: http://seqanswers.com/forums/showthread.php?p=3505

Basically, ELAND doesn't allow for different lengths and Bowtie does.

[danielsbrewer]

bowtie error

I am just starting out with bowtie and I am getting the following error:

$ ./bowtie -p 4  -t h_sapiens ../GDB1.fastq GDB1.map
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:02
Error: Read (Error: Read (Error: Read (Error: Read (HHHHWWWWIIII----EEEEAAAASSSS222266669999BBBB::::5555::::1464::::711344088362:84:1::1818164431573) is less than 2 characters long7) is less than 2 characters long) is less than 2 characters long) is less than 2 characters long

Has anyone seen anything similar or know what its actually saying. I am pretty sure that the smallest read size is something like 10.

[Ben Langmead]

That sounds like an issue with how the read file is formatted. Can you share that file with me, e.g. via email (langmead at umd dot edu)? I can take a quick look.

[danielsbrewer]

Is Bowtie suitable for miRNA detection

I am just playing around with bowtie along with other software (maq,novoalign) and was wondering whether bowtie is suitable for use with an miRNA detection experiment. In a previous post Ben states that:

First, let me reemphasize that I think of Bowtie's target application as mammalian resequencing - that's how I characterize it in the manual and that's what we spend our time trying to optimize it for.

That hints to me that the default options might not be the best for experiments to compare miRNAs between samples. Does anyone have an opinion as to what the best options to use are?

I would think that you want to know all the alignments for each read above a certain quality threshold. At the moment I am thinking of using "--best -k 100", as if there is more that 100 hits then it is probably not a "real" alignement.

Any thoughts?

[ieuanclay]

Hi Ben, Just to say bowtie is great work. Far outstrips any pipeline we have used previously!
One question though - is there a way to output reads with multiple hits to a separate file? We work on repetitive regions and with a little massaging, this data may still be useful to us.

[Ben Langmead]

Thanks!

Have you checked out the -m and --maxfa/--maxfq options?

[ieuanclay]

Doh... Your patience obviously exceeds mine...

I was confused by the default for -m being unlimited - does this mean that without --maxfa being set, your mapped output will include sequences with mulitple hits?

[Ben Langmead]

Yes - if you specify -k > 1 or -a, Bowtie will output the appropriate number of hits per read for reads with >=1 hit. If -m <int> is also specified, Bowtie will output no alignments for reads with > <int> alignments and, if --maxfa/--maxfq is specified, will dump those reads (the reads, not the alignments) to the specified file. For reads with <= <int> alignments, Bowtie behaves the same as if -m were not specified.

I hope that helps.