tophat total alignment

[zorph]

does anyone know how to compute total alignment from TopHat. I have 5 files marked file*****.log and they all have the following format:
# reads processed: 7069046
# reads with at least one reported alignment: 710849 (10.06%)
# reads that failed to align: 6227028 (88.09%)
# reads with alignments suppressed due to -m: 131169 (1.86%)
Reported 2269253 alignments to 1 output stream(s)


my reads were 50bp and Tophat divided these into segment lengths of 25bp.

[shurjo]

does anyone know how to compute total alignment from TopHat. I have 5 files marked file*****.log and they all have the following format:
# reads processed: 7069046
# reads with at least one reported alignment: 710849 (10.06%)
# reads that failed to align: 6227028 (88.09%)
# reads with alignments suppressed due to -m: 131169 (1.86%)
Reported 2269253 alignments to 1 output stream(s)


my reads were 50bp and Tophat divided these into segment lengths of 25bp.

It would be useful if you define "total alignment" a bit more precisely.

[zorph]

my definition of total alignment are all of the reads that can be aligned to the genome.

I don't care if they're used to make transfrags in the cufflinks algorithm..

[Thomas Doktor]

Then you're interested in this line:
# reads with at least one reported alignment: 710849 (10.06%)

This is a very low mapping ratio, even for an RNA-seq aligner, are there a lot of bad quality reads? Are you sure you mapped to the right species (e.g. human instead of mouse, as sometimes happens for me...) ?

[zorph]

my other 4 file***.log files have much better alignment percentages.

However, when i add the total amount of reads (from the reads processed line, eg. # reads processed: 7069046) from all 5 files, they go well above the # of reads I input to tophat.