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Old 10-27-2015, 04:15 PM   #4
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,966

Have you set the file format to "fastqsanger" for your original data files (I can't tell from the history you shared). Here is how you would do it: Then you should not have to groom your data. If this is recent data correct so it should already be in sanger fastq format.

It appears that part of illumina fastq header (1:N:0:18) is missing from the reads that appear to have an alignment (at least that is what it looks like in the web page).
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