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Name Modified Size InfoDownloads / Week
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getRightReads.py 2014-11-18 1.1 kB
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getInputFromSAMofBWA.py 2014-11-18 2.2 kB
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getInputFromSAMNoclip.py 2014-11-18 1.5 kB
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readme_script.txt 2014-11-18 668 Bytes
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Totals: 4 Items   5.5 kB 0 
getInputFromSAMofBWA.py is used to get input from the SAM generated by BWA.

usage: python getInputFromSAMofBWA.py file.sam input_anchor.txt input.fastq

getInputFromSAMNoclip.py is used to get input from a sorted SAM file without softclip. For the not mapped reads, if they are the original sequence, then the output is correct. If you are using the SLX MAQ, then use the getRightReads.py to correct the fastq file. 

usage: python getInputFromSAMNoclip.py file.sam input_anchor.txt input.fastq

getRightReads.py is used with getInputFromSAMNoclip.py when the alignment is SLX format. 

usage: python getRightReads.py input_anchor.txt input.fastq correct_input.fastq
Source: readme_script.txt, updated 2014-11-18