Visualizing Bowtie results in Galaxy

[sugo]

Hello,

I have just done my very first run of bowtie, via galaxy. I want to get an idea of whether it worked at all... but I have no idea what the output means! Anyone know of a good link(s) to explain the galaxy output of bowtie?

When I click the little 'view data' button, I get an output like this:

QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT
@HD VN:1.0 SO:unsorted
@SQ SN:chr2 LN:30794189
@SQ SN:chr3 LN:19779522
@SQ SN:chr4_group4 LN:6586962

I know that QNAME etc. describe various features of the output, but I don't know what exactly they mean or how they may or may not be linked to the many lines of text that come after them (the first four of which I've included here... and which after about 16 lines all look something like this one: @SQ SN:Unknown_group_1 LN:174220).

I also tried to visualize the data through Trackster, but I'm getting this error:

"The page at https://usegalaxy.org says: Could not load chroms for this dbkey"

It seems to me that this is an error with galaxy and the reference genome (which is one of the built-in references), but I don't know how to go about resolving it.

Thanks in advance for any advice.

[GenoMax]

Are you using a local mirror of galaxy or the public install at PSU?

[sugo]

I'm using the main galaxy server, as far as I know (https://usegalaxy.org).