tophat - basic question - mapped reads

[chrisbala]

I have just done my first attempts at mapping reads/splice junctions with tophat and bowtie.

When bowtie is run independently, you get some nice feedback like:
# reads processed: 10722718
# reads with at least one reported alignment: 3811383 (35.54%)
# reads that failed to align: 6911335 (64.46%)

when tophat is run, i can't find this output from bowtie anywhere? so i tried counting the lines in the .sam file. But does the sam have multiple lines for reads that are mapped more than once?


Thanks!

[dan]

I'd like to get an answer to the same question. How many additional reads does TopHat align over bowtie?

[chrisbala]

more generally

I am also generally curious about the % mapped reads. The people who sit in the desks around me are getting fairly similar numbers (kind of low in my opinion?). Can anyone comment on what others are getting? The genome I'm working with is fairly chopped up still, but 34% seems kind of sad?

[dan]

I'm seeing like 60 - 70% mapped by Bowtie alone, and an unknown improvement from TopHat.

This is with ~70 bp illumina reads.