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Old 10-26-2015, 04:27 PM   #1
Location: Australia

Join Date: Aug 2014
Posts: 25
Default SAM file after Bowtie is messed up


I have chip-seq data from E. coli (51 bp). I mapped my fastq file to my reference genome (custom build) using Bowtie in Galaxy. In the SAM output file, some rows have the sequence in the quality score columns, and the quality scores in the OPT column. Some rows are fine.

Anyone would know what is causing it and how to fix that ?

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