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BWA input file in sanger format doubts..
I keep getting segmentation fault when I try using maq to convert solexa to sanger fastq format. I tried with a small data set to convert solexa to sanger format using galaxy and bwa works perfectly fine without any segmentation fault. Since I am handling huge data set, using Galaxy to convert the format is not feasible.
Hence how to groom solexa sequence.txt into sanger format hence BWA will not give any errors during generating alignment steps (samse or sampe). Thanks.
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