hiii all
After running Bowtie2 i got the output in SAM format. i am actually dealing with paired ends and has given a --very-sensitive preset to align my reads in the output i can see smthg like YF:Z:UP where Value of UP indicates the read was part of a pair but the pair failed to aligned either concordantly or discordantly for certain number of alignments. my question is even though i have mentioned in the options during run that only pairs that follow the strict criteria have to be displayed y is my output file contain the unaligned reads?
After running Bowtie2 i got the output in SAM format. i am actually dealing with paired ends and has given a --very-sensitive preset to align my reads in the output i can see smthg like YF:Z:UP where Value of UP indicates the read was part of a pair but the pair failed to aligned either concordantly or discordantly for certain number of alignments. my question is even though i have mentioned in the options during run that only pairs that follow the strict criteria have to be displayed y is my output file contain the unaligned reads?
