Dinh/Dinh 2013/NOTES/2013-6-24: Difference between revisions

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===COPE results===
===COPE results===
{| {{table}} border=0.5
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''index'''
| align="center" style="background:#f0f0f0;"|'''total_pairs'''
| align="center" style="background:#f0f0f0;"|'''total_pairs'''
| align="center" style="background:#f0f0f0;"|'''connected_pairs'''
| align="center" style="background:#f0f0f0;"|'''connected_pairs'''
Line 23: Line 24:
| align="center" style="background:#f0f0f0;"|'''low_quality_ratio(%)'''
| align="center" style="background:#f0f0f0;"|'''low_quality_ratio(%)'''
|-
|-
| 546091||37624||6.88969||239413||43.8412
| 1||546,091||37,624||6.88969||239413||43.8412
|-
|-
| 1201482||76332||6.35315||603335||50.2159
| 2||1,201,482||76,332||6.35315||603335||50.2159
|-
|-
| 2107061||120889||5.73733||1155859||54.8565
| 3||2,107,061||120,889||5.73733||1155859||54.8565
|-
|-
| 2416376||157448||6.51587||1124046||46.5178
| 4||2,416,376||157,448||6.51587||1124046||46.5178
|-
|-
| 2699273||191332||7.08828||1138412||42.1748
| 5||2,699,273||191,332||7.08828||1138412||42.1748
|-
|-
| 1576107||100314||6.36467||805229||51.0897
| 6||1,576,107||100,314||6.36467||805229||51.0897
|-
|-
| 2025366||131396||6.48752||990421||48.9008
| 7||2,025,366||131,396||6.48752||990421||48.9008
|-
|-
| 546091||35800||6.55568||239459||43.8497
| 8||546,091||35,800||6.55568||239459||43.8497
|}
|}

Revision as of 20:47, 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

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