Bowtie2 alignment rate

Question

[pavithraashokkumar818]

Hello,

I'm trying to align my RNA seq data of hydra (which has an algal symbiont within it ) to its algal symbiont using bowtie, my alignment rate was 0.07%, is that inacurrate because I saw that good alignment rate is more than 70%. can you guys please help me with this?

[jeevii]

Hello,

just wanted to ask, have you followed Ribo depletion based library?

If yes, just try aligning your data against non-coding sequences to remove contamination. Then you can align the un-mapped reads to your reference genome and check . This process helps ensure the removal of unwanted RNA species, particularly ribosomal RNA and other non-coding RNAs present in the sample.

If you have not followed ribo depletion based library, just try and execute BWA aligner to confirm the results.

Thanks!