I used Bowtie2 to build an index for a single human chromosome for subsequent RNA Seq analysis, as that’s all I’m interested in right now, and I figured that would help make alignments faster. I ran Bowtie2-inspect (-s option) and see an Output different from that listed in the Bowtie2 Manual (under Bowtie-inspect, toward the bottom). See here:
There are 2 variables that aren’t listed in the manual: ‘Flags’ and ‘Reverse Flags’. Any idea what these are? And more important, do the flags and/or their values indicate a problem?
Flags 1
Reverse flags 5
Colorspace 0
2.0-compatible 1
SA-Sample 1 in 16
FTab-Chars 10
Sequence-1 chr4 191154276
Reverse flags 5
Colorspace 0
2.0-compatible 1
SA-Sample 1 in 16
FTab-Chars 10
Sequence-1 chr4 191154276
There are 2 variables that aren’t listed in the manual: ‘Flags’ and ‘Reverse Flags’. Any idea what these are? And more important, do the flags and/or their values indicate a problem?
