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