Dinh/Dinh 2013/NOTES/2013-6-24

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Revision as of 20:45, 24 June 2013 by >Dinh
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Analysis of Blueprint MiSeq Run

  • 2 X 250bp MiSeq PE run

Pre-processing

  • Obtain UMI from the first 10bp of read 1, label both reads with UMI
  • Trim 27 bp from 5 prime end of read 1 and read 2
  • Create kmer_table for COPE
  • Use COPE to combine overlapping read 1 and read 2
for f in 1Index1_S1 1Index2_S2 1Index3_S3 2Index4_S6 1Index5_S4 2Index6_S7 2Index7_S8 1Index8_S5
do

	./getUMI.pl 130620_MiSeq/TES1-${f}_L001_R1_001.fastq 130620_MiSeq/TES1-${f}_L001_R2_001.fastq $f
	~/softwares/cope-src-v1.1.3/src/cope -a $f.R1.fq -b $f.R2.fq -o $f.fq -2 $f.leftR1.fq -3 $f.leftR2.fq -m 1  -t kmer_table.freq.cz -f kmer_table.freq.cz.len >cope.$f.log 2>cope.$f.error
	rm $f.R1.fq $f.R2.fq
done

COPE results

total_pairs connected_pairs connect_ratio(%) low_quality_pairs low_quality_ratio(%)
546091 37624 6.88969 239413 43.8412
1201482 76332 6.35315 603335 50.2159
2107061 120889 5.73733 1155859 54.8565
2416376 157448 6.51587 1124046 46.5178
2699273 191332 7.08828 1138412 42.1748
1576107 100314 6.36467 805229 51.0897
2025366 131396 6.48752 990421 48.9008
546091 35800 6.55568 239459 43.8497