Good morning,
I am doing a de novo transcriptome assembly from two samples x_R1.fastq and x_R1.fastq. The fact is that I filter the samples and make two assemblies, one with SPAdes and one with Trinity. When I use bowtie2 to find out the alignment percentage of the reads x_R1.fastq and x_R1.fastq to the final assemblies I get the following:
SPAdes assembly: 92.75%
Trinity assembly: 92.77%
But when using Evigene's tr2aacds4.pl script to get a single redundant assembly from the first assembly, the alignment percentage drops to: 33.72%, and I don't understand it.
Could you help me understand it? Is it normal for this to happen?
Thank you so much,
Karen.
Good morning, I am doing a de novo transcriptome assembly from two samples x_R1.fastq and x_R1.fastq. The fact is that I filter the samples and make two assemblies, one with SPAdes and one with Trinity. When I use bowtie2 to find out the alignment percentage of the reads x_R1.fastq and x_R1.fastq to the final assemblies I get the following:
Could you help me understand it? Is it normal for this to happen? Thank you so much, Karen.