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