Typical Bowtie2 Alignment Rates

[tdyo]

Hi all,

I'm working with Bowtie2 to map Illumina paired-end filtered reads to a non-model reference transcriptome (same species) that was assembled denovo (SOAPdenovo) from prior sequencing results. A typical output is as follows, but I get the impression that I'm getting pretty high alignment rates.

Time loading reference: 00:00:00
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:01
Multiseed full-index search: 01:09:11
31453955 reads; of these:
  31453955 (100.00%) were paired; of these:
    14583671 (46.37%) aligned concordantly 0 times
    14468481 (46.00%) aligned concordantly exactly 1 time
    2401803 (7.64%) aligned concordantly >1 times
    ----
    14583671 pairs aligned concordantly 0 times; of these:
      7284303 (49.95%) aligned discordantly 1 time
    ----
    7299368 pairs aligned 0 times concordantly or discordantly; of these:
      14598736 mates make up the pairs; of these:
        8811722 (60.36%) aligned 0 times
        2753409 (18.86%) aligned exactly 1 time
        3033605 (20.78%) aligned >1 times
85.99% overall alignment rate
Time searching: 01:09:14
Overall time: 01:09:18

I have found some other results here on SEQanswers here and here, and they seem to be in line. The overall alignment from the example in the Bowtie2 manual is also in the 90% range.

So are these 70%-90% overall alignment rates typical or should I be concerned? Thanks in advance for any feedback.

[shi]

If you are mapping RNA-seq reads, you probably better use TopHat because TopHat is a splice-aware aligner. Alternatively, you can try Subread that is a newly developed splice-aware aligner.

[oiiio]

Here are a BUNCH of benchmarks on bowtie2 over a number of different sequencing platforms

http://www.bioplanet.com/gcat/report-list/public-1/search-bowtie

[maivantan]

dear all,
I used bowtie2 for processing miseq data. I have one question that how can i use command for file that containing barcode adapters and list of materials.

Any suggestions ?
Thank you very much