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?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
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
Comment
-
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
Comment
-
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?
Comment
-
Originally posted by danielsbrewer View PostDoes 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?
-Adam
Comment
-
Originally posted by danielsbrewer View PostDoes 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?
Basically, ELAND doesn't allow for different lengths and Bowtie does.
Comment
-
bowtie error
I am just starting out with bowtie and I am getting the following error:
Code:$ ./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
Comment
-
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:
Originally posted by Ben Langmead View PostFirst, 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.
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?
Comment
-
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.
Comment
-
-
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.
Comment
Latest Articles
Collapse
-
by seqadmin
Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...-
Channel: Articles
10-18-2024, 07:11 AM -
-
by seqadmin
Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.
Nobel Prize for MicroRNA Discovery
This week,...-
Channel: Articles
10-07-2024, 08:07 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
New Model Aims to Explain Polygenic Diseases by Connecting Genomic Mutations and Regulatory Networks
by seqadmin
Started by seqadmin, Yesterday, 05:31 AM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 05:31 AM
|
||
Started by seqadmin, 10-24-2024, 06:58 AM
|
0 responses
20 views
0 likes
|
Last Post
by seqadmin
10-24-2024, 06:58 AM
|
||
New AI Model Designs Synthetic DNA Switches for Targeted Gene Expression in Specific Cell Types
by seqadmin
Started by seqadmin, 10-23-2024, 08:43 AM
|
0 responses
48 views
0 likes
|
Last Post
by seqadmin
10-23-2024, 08:43 AM
|
||
Started by seqadmin, 10-17-2024, 07:29 AM
|
0 responses
58 views
0 likes
|
Last Post
by seqadmin
10-17-2024, 07:29 AM
|
Comment