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Old 02-28-2011, 10:15 AM   #1
zack80.liu
Junior Member
 
Location: TX

Join Date: Feb 2011
Posts: 9
Default Percentage of mapped reads ?

Hi all,

I am new to the RNA seq world. I have processed bunch of illumina paired end reads. The reported alignment is only 49%.. I was wondering if this is normal. Here's the command and output. Thanks.

bowtie -n 3 -p 10 --best -e 200 --trim5 15 --trim3 25 --sam BowtieIndexes/mm9 -1 Raw_files/sample-1_export.fq -2 sample-2_export.fq sample.sam


# reads processed: 21482797
# reads with at least one reported alignment: 10637665 (49.52%)
# reads that failed to align: 10845132 (50.48%)
Reported 10637665 paired-end alignments to 1 output stream(s)
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