Bowtie Alignment

Question

[gandham71]

Using bowtie2-build i constructed an index using the reference genome (Newcastle disease virus - already available). Then I used this index to align my Iontorrent single reads to the index. Only nine percent got aligned. I opened the sam file and used one of the sequences which has not aligned to the reference in blastn and it perfectly matched to NDV. What should I do and how should I interpret?

[k.nirmalraman]

can you build the transcriptome index and then do the alignment? And another reason is possible introns which would not bowtie to align the reads... so trying Tophat is another option if you know this information,,,

[Matt LaFave]

What settings did you use? For example, -n vs. -v mode, etc.

[JC]

IonTorrent have a lot of sequence errors, bowtie will require to allow more mismatches to align correctly, one alternative option is to use Blat.