Hi Community user,
I have single-end reads fastq file. I have generated denovo assembly using velvet/oases. Now i need to check, how good is my assembly. So I am using aligner, bowtie. But I am confused which fasta file to use for creating bowtie index i.e. shall I used contigs.fa from velveg or transcript.fa file from oases. Do you guys prefer --best parameter option while running bowtie?
I would really appreciate your feedback and reponse.