Thank you jennaj.
I have assembled the reads using Trinity, after filtering them according to the blastn results. but now that I try to align back those filtered reads to the assembled transcriptome using Bowtie2 (to assess the quality of the assembly), I get an error message: " Error, fewer reads in file specified with -2 than in file specified with -1". I noticed that the number of reads in each forward doesn’t match the number of its reverse.
What shall I do??
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