This might be a silly question but it is bugging me and I need the answer. I have a set of paired end FASTQ files that contain about 30 million reads total. After aligning them with BWA and sorting the output with samtools, the resulting BAM file now has about 72 million reads. Why????
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Both come from iterating the files in Python. The FASTQ files are read in in blocks of four lines each which is one read. This example is a MiSeq run so 30 million (15 million in each FASTQ) seems realistic. The BAM count is from
bamfile = pysam.AlignmentFile(o['bamfile'], "rb")
bamfile.count()
or
bamfile_reads = functools.reduce(lambda x, y: x + y, [eval('+'.join(l.rstrip('\n').split('\t')[2:])) for l in pysam.idxstats(o['bamfile'])])
or simply counting the reads as I iterate the BAM file to do my analysis.Last edited by pkMyt1; 05-12-2015, 08:36 AM.
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Originally posted by Brian Bushnell View PostThat depends on the goal of your experiment. What are you trying to do?
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