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Old 10-27-2015, 05:26 PM   #5
Location: Australia

Join Date: Aug 2014
Posts: 25


thank you for looking at my data.

I have tried without grooming, just changing data type (my reads are illumina 1.9 encoding) and I have the exact same result.

The illumina fastq header (1:N:0:18) is present for all reads in the fastq file.

I have tried galaxy GVL instance and galaxy main. Same results.

I don't have this problem when I use BWA mapping. But it's better to use Bowtie for E. coli reads since BWA looks for intron so better used for eukaryotes is that right ?
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