I am running Bowtie (0.12.5) with the --sam option. The output file contains non-aligned reads. I thought the SAM file was only supposed to contain aligned reads? Am I doing something wrong?
Here is the command I'm running:
Here is one of the lines I'm referring to:
Thank you,
Lee
Here is the command I'm running:
Code:
bowtie -p 4 -t -a --solexa1.3-quals --minins 0 --maxins 500 -m 5 --sam ./bowtie_indexes/hg18 -1 foo1 -2 foo2 > output.txt
Code:
GAII_0001:1:1:1145:8968#0 141 * 0 0 * * 0 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN #################################################################################################### XM:i:0
Lee
Comment