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Perl to extract from a pdf
04-30-2017
. Reads1 is IonXpress 004 with the Reads value extracted Reads2 is IonXpress 005 with the Reads value extracted Reads3 is IonXpress 006 with the Reads value extracted NoBarcode is No Barcode with the Reads value extracted
Barcode Name Sample Bases ≥ Q20 Reads Mean Read Length
No barcode none 151,751,086 122,614,710 844,020 180 bp
IonXpress 004 00-0000 Last- 8,373,945,632 7,188,703,690 38,774,136 216 bp
First
) * 100
IonXpress 005 00-0001 LastN- 5,226,515,080 4,502,314,522 24,025,446 218 bp
FirstN
IonXpress 006 00-0002 La- 6,651,737,354 5,681,526,265 30,850,757 216 bp
Fiperl -ne 'BEGIN{print join("\t","ReadLength", "UsableSequence", "Polyclonal", "LowQuality", "UnalignedBases", "Barcode1", "Barcode2", "Barcode3", "NoBarcode", "Exception"),"\n"};s/[\%\,]//g;@f=split/\s+/> ;/Key Signal/ and ($ks,$tr,$rl)=@p[3..5];/Usable/ and ($il,$us)=@p[1,2];/Polyclonal/ and $pc=$f[-1];/Low Quality/ and $lq=$f[-1];/Unaligned Reads/ and $ur=$f[-1] and print join("\t",$rl,$us,$pc,$lq,$ur,$f[-1]," "),"\n";@p=@f' run.txtReadLength UsableSequence Polyclonal LowQuality UnalignedBases Barcode1 Barcode2 Barcode3 NoBarcode Exception 216 68 27.5 04.7 0.6 0.6
ReadLength UsableSequence Polyclonal LowQuality UnalignedBases Barcode1 Barcode2 Barcode3 NoBarcode Exception
216 68 27.5 4.7 0.6 8774136 24025446 30850757 0.89
(Reads / TotalReads) * 100|
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