Originally posted by juanita
View Post
You can also grab 100 reads, turn them into fasta format and do blastn with them (if online use the blastn rather than megablast option) and see read by read what is in there.
Other options...your sample is not highly related to the reference, the reference may be incomplete and missing regions, the reference is lacking high copy repeat content like mtDNA or chloroplast and many reads go to those.
Leave a comment: