Hi my command for a paired end read is as follows:
./bowtie -v 0 -a -p 2 -X 300 hg19 -c -1 TGGGAGATATACCTAATGCTAGATGACCCA, -2 AAGTTTAGGGTACATGTGCAGGTTAGTTA
and am getting a message that says
reads that failed to align - 1(100%)
am not sure if am going wrong with the syntax.it works when I do them as single-end reads.
help!!
thanks
./bowtie -v 0 -a -p 2 -X 300 hg19 -c -1 TGGGAGATATACCTAATGCTAGATGACCCA, -2 AAGTTTAGGGTACATGTGCAGGTTAGTTA
and am getting a message that says
reads that failed to align - 1(100%)
am not sure if am going wrong with the syntax.it works when I do them as single-end reads.
help!!
thanks
Comment