Work Log 12/28

Transcript

1. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 1 C l i p To o l Te s t  Week Progress 12/28
2. Previous result by fastx_clipper Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 2 0.E+00 1.E+07 2.E+07 3.E+07 4.E+07 5.E+07 6.E+07 SRR372611 SRR372612 SRR372613 SRR372614 SRR372615 SRR372616 SRR372617 SRR372618 SRR372619 SRR372620 SRR372621 SRR372622 SRR372623 SRR372624 SRR372625 SRR372626 SRR372627 SRR372628 SRR372629 SRR372630 SRR372631 SRR372632 SRR372633 SRR372634 SRR372635 SRR372636 SRR372637 SRR372638 SRR372639 SRR372640 SRR372641 SRR372642 SRR372643 SRR372644 SRR372645 SRR372646 SRR372647 SRR372648 SRR372649 SRR372650 SRR372651 SRR372652 SRR372653 SRR372654 SRR372655 SRR372656 SRR372657 SRR372658 SRR372659 SRR372660 SRR372661 SRR372662 SRR372663 SRR372664 SRR372665 SRR372666 SRR372667 SRR372668 SRR372669 SRR372670 SRR372671 SRR372672 read count
   N reads non-clipped adapter-only too-short output
3. fastx_clipper vs cutadapt  Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 3 fastx_clipper cutadapt sample clipped ratio too-short ratio clipped ratio too-short ratio SRR372612 49.9% 4.3% 48.9% 1.4% SRR372617 92.1% 1.4% 91.7% 1.2% SRR372643 46.5% 3.3% 42.5% 0.7% SRR191395 99.3% 0.2% 93.6% 0.0% SRR191434 96.4% 1.0% 80.1% 0.0% SRR191443 99.3% 0.1% 78.9% 0.0% SRR191623 98.7% 0.9% 91.2% 0.0% SRR191624 98.7% 0.8% 93.9% 0.0% SRR191629 98.7% 6.3% 94.0% 0.0% SRR191634 98.8% 0.1% 95.4% 0.0% problem of sample itself
4. cutadapt •  able to clip adapter from both 3’, 5’ •  allow adapter mismatch •  Ex. mismatch rate = 10% •  No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-22 bp: 2 •  covers all functions that fastx_clipper has •  slightly slower than fastx_clipper Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 4