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Old 07-06-2012, 03:30 PM   #5
Location: Cambridge, MA

Join Date: Apr 2011
Posts: 18

If you go with the conversion tool, it would also be useful if it could convert from, say, hg18 to hg19 using a liftover file.

My vote would be for a Python wrapper to bowtie or bwa. For example, I often have barcoded data and would like to write a loop that reads a fastq file, removes the barcode, aligns the read, and then uses pysam to write it to a different bam file depending on the barcode. This would also give me more control over how multiply aligned or mispaired reads are handled, or let me store additional information with the alignment.
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