Dinh/Dinh 2013/NOTES/2013-6-24
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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
index | total_pairs | connected_pairs | connect_ratio(%) | low_quality_pairs | low_quality_ratio(%) |
1 | 546,091 | 37,624 | 6.88969 | 239413 | 43.8412 |
2 | 1,201,482 | 76,332 | 6.35315 | 603335 | 50.2159 |
3 | 2,107,061 | 120,889 | 5.73733 | 1155859 | 54.8565 |
4 | 2,416,376 | 157,448 | 6.51587 | 1124046 | 46.5178 |
5 | 2,699,273 | 191,332 | 7.08828 | 1138412 | 42.1748 |
6 | 1,576,107 | 100,314 | 6.36467 | 805229 | 51.0897 |
7 | 2,025,366 | 131,396 | 6.48752 | 990421 | 48.9008 |
8 | 546,091 | 35,800 | 6.55568 | 239459 | 43.8497 |