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 with PROKKA 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 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.
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 with PROKKA 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 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.
Can you please help me on this issue.
Thank you so much