Hello,

I performed whole genome sequencing of pure culture bacteria using linux tools. I used sickle, megahit, bbmap and then metabat for binning process. I got the bin which is 98% completed (using CHECKM). I input the obtained bin for annotation in PATRIC and downloaded the fasta file from the output.

I mapped the downloaded fasta file with the transcriptomes of same pure culture bacteria. The transcriptomes were quality filtered (rRNA were removed, contaminants were removed). The mapping was very low (~1%).

I even tried annotation of bin with prokka and then mapped the downloaded fasta file (from Prokka) with transcriptomes. The mapping is still very low.

I am not sure why the mapping is low even though the bin and transcriptomes belong to same bacteria. I tried to use bowtie2, bbmap for allignment but still mapping is very low. I tried multiple times. I am not sure where I am going wrong.

Can you please help me on this issue.

Thank you so much