Dinh/Dinh 2013/NOTES/2013-6-24: Difference between revisions
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>Dinh (Created page with "=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...") |
>Dinh mNo edit summary |
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=Analysis of Blueprint MiSeq Run= | =Analysis of Blueprint MiSeq Run= | ||
* 2 X 250bp MiSeq PE run | * 2 X 250bp MiSeq PE run | ||
==Pre-processing== | |||
* Obtain UMI from the first 10bp of read 1, label both reads with UMI | * 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 | * Trim 27 bp from 5 prime end of read 1 and read 2 | ||
Line 15: | Line 15: | ||
done | done | ||
</nowiki> | </nowiki> | ||
===COPE results=== | |||
{| {{table}} border=1 | |||
| align="center" style="background:#f0f0f0;"|'''total_pairs''' | |||
| align="center" style="background:#f0f0f0;"|'''connected_pairs''' | |||
| align="center" style="background:#f0f0f0;"|'''connect_ratio(%)''' | |||
| align="center" style="background:#f0f0f0;"|'''low_quality_pairs''' | |||
| align="center" style="background:#f0f0f0;"|'''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 | |||
|} |
Revision as of 20:45, 24 June 2013
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 |