Cant get bowtie to work

HI there,
Im a first time sequencer…Im using BOWTIE2 and have sequenced B. longum & its passed the QC part but now no matter what reference I use it comes back with 0.0% overall alignment, please help ??
Eleana

Hi @Eleana,

Do you use B. longum genome in your history? Have you changed Source of reference genome to In History during bowtie2 job setup? If yes, Blast one read sequence against bacteria db. Do you see B. longum in output? If not, Blast more reads.

Hope that helps.

Kind regards,
Igor

Hi Igor

Your advice help and I got it to align, thank you so much

Kind regards,

Eleana