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!
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!
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