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Sequence File Formats

Sequence File Formats. Sequencing – the old way. G. A. T. C. di - deoxy chain terminators (G, A, T, C) 4 different reactions 35 S dCTP Electrophoresis through an acrylamide gel Transfer gel to blotting paper Expose to X-ray film Develop film and read sequence.

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Sequence File Formats

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  1. Sequence File Formats

  2. Sequencing – the old way G A T C • di-deoxy chain terminators (G, A, T, C) • 4 different reactions • 35S dCTP • Electrophoresis through an acrylamide gel • Transfer gel to blotting paper • Expose to X-ray film • Develop film and read sequence

  3. Chromatograms – Sanger sequencing • Fluorescent di-deoxy chain terminators • Four nucleotides, four “colors” • Electrophoresis through a polymer • Read the colors as they pass through a laser/detector

  4. Flowgrams, Ionograms • Flow nucleotides through a reaction cell – one at a time • Detect byproducts of incorporation • 454 sequencing, pyrophosphate (light) • Ion Torrent, hydrogen ions (pH)

  5. Colorspace – SOLiD sequencing • Sequence by ligation (detects 2 bases/cycle) • Flow 4 pools of 4 oligonucleotides over the reaction wells (each pool is labeled with a different fluorescent dye) • Detect dye, cleave off oligo-dye adaptor and repeat

  6. Process is repeated using nested primers

  7. SOLiD color codes AT

  8. Colorspace csfasta 2nd base 1st base

  9. fasta, multifasta • .mfa, .mpfa • Fasta (.fasta, .fa, .fas, .fsa, .fna) >Sequence1 CAATCATAGAGACAGCTGTTGTATCGTTACGTCATTCATGCAAGACCGCATTTAACGGCCAAGGCATTTCGCTACCTTAG • Multifasta (.mfa, .mpfa) >Sequence1 CAATCATAGAGACAGCTGTTGTATCGTTACGTCATTCATGCAAGACCGCATTTAACGGCCAAGGCATTTCGCTACCTTAG >Sequence2 ACCAGGAAGGTGGCCGACGCCAGCCGCTGATGCCACTCCACCCGCCGCGCACCGAGTCCAGGAGCGCGGACAAGGGGATT

  10. Colorspacefasta • .csfasta >Sequence1 T0123020301120301012020212330213230 >Sequence2 T2130322221303120001320310030123123 2nd base A C G T 0 1 2 3 A 1 0 3 2 C 2 3 0 1 1st base G 3 2 1 0 T

  11. Sequence Quality • Some sequence calls have better quality than others

  12. Quality values • Q = -10 log10P Q = qualityvalue P = probabilityoferror

  13. .sff files .sff^@^@^@^A^@^@^@^@^@^@^@^@^@^@^@^@^@^Vp<D8>^B0^@^D^B^H^ATACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCAG^@^@^@^@^@^@ ^@^K^@^@^@4^@^E^@%^@^@^@^@PXDEO:13:42^@^@^@^@^@^@4^@^A^@q^@^@^@^A^@f^@^H^@<E0>^@^A^@p^@ESC^@^@^@j^@j^@^@^@k^@<C3>^@^Z^@K^@^@^@l^@^A^@c^@x^@^@^@^@^@^A^@^@^@g^@^A^@i^@^@^@^@^@j ^@^A^@<E2>^@^@^@^@^@u^@^@^@i^@^@^@^@^@|^@b^@r^@^M^@T^@^@^@O^@^@^@^@^@B^@^@^@3^@^@^@^@^@^@^@^B^@^B^AS^@<F1>^@ <B1>^@L^@^B^@b^@3^@^@^@^B^@3^@3^@^@^@^@^@^B^@^C^@^B^@w^A<E3>^@^@^@^H^@`^@^A^@^@^@a^@^@^@^B^A^E^@^@^@^@^@^@^@^B^@^@^@^G^@^B^@^@^@^B^@^B^@^B^@^B^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^A^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^A^B^C^B^@^B^C^A^B^A^@^B^B^B^A^E^B^C^B^@^C^B^C^A^A^B^B^C^B^F^@^@^A^@^A^@^A^B^A^C^A^F^A^@^@^@^@^C^C^C^@^@TCAGGCAGATTGTGACGAGGCTGAGACTGCCCAAGGCACACAGGGGGTAGGG^M^L^Q^Z^S^YESC^]^]^_^Y^T^Y^W^\^]^_ESCESC^VESC^Z^Z^U^X^T^W^O^L^L^L^F ^G ^P^L ^L ^L^P^P^P^R^F^R ^L^L^L^F^@^@^@^@^@ ^@^K^@^@^@'^@^E^@^X^@^@^@^@

  14. Roche 454 .sff Files – common header Magic Number: 0x2E736666
Version: 0001
Index Offset: 110544
Index Length: 3173
# of Reads: 35
Header Length: 840
Key Length: 4
# of Flows: 800
Flowgram Code: 1
Flow Chars: TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG
Key Sequence: TCAG

  15. .sff files - sequence specific information • >F7K88GK01BMPI0
Run Prefix: R_2009_12_18_15_27_42_
Region #: 1
XY Location: 0551_2346 • Run Name: R_2009_12_18_15_27_42_FLX########_Administrator_yourrunname
Analysis Name: D_2009_12_19_01_11_43_XX_fullProcessing
Full Path: /data/R_2009_12_18_15_27_42_FLX########_Administrator_yourrunname/D_2009_12_19_01_11_43_XX_fullProcessing/ • Read Header Len: 32
Name Length: 14
# of Bases: 500
Clip Qual Left: 15
Clip Qual Right: 490
Clip AdapLeft: 0
Clip AdapRight: 0 • Flowgram: 1.03 0.00 1.01 0.02 0.00 0.96 0.00 1.00 0.00 1.04 0.00 0.00 0.97 0.00 0.96 0.02 0.00 1.04 0.01 1.04 0.00 0.97 0.96 0.02 0.00 1.00 0.95 1.04 0.00 0.00 2.04 0.02 0.03 1.05 0.99 0.01 2.84 0.03 0.05 0.97 0.12 0.00 1.01 0.05 0.97 0.01 2.89 0.04 0.09 1.05 0.15 0.00 2.84 0.06 1.00 0.01 0.13 1.01 0.09 0.98 0.01 0.05 1.01 0.06 0.00 1.04 3.72 0.03 0.00 0.96 1.97 0.04 0.01 1.97 0.12 0.98 0.02 0.08 0.95 0.12 ...
FlowIndexes: 1 3 6 8 10 13 15 18 20 22 23 26 27 28 31 31 34 35 37 37 37 40 43 45 47 47 47 50 53 53 53 55 58 60 63 66 67 67 67 67 70 71 71 74 74 76 79 82 83 86 86 88 88 91 93 96 97 99 102 105 ...
Bases: tcagatcagacacgCCACTTTGCTCCCATTTCAGCACCCCACCAAGCACAAGGCTGTCATCCCAATTGGACGGACAGATATGAGGTTAGCATTGGAAACCAATTCAGTCCCTAATTATTCACGACTGAACCCAGCGACAATTGGACATGGATTCATTTTTCAACTTGATTTGTTGTTGTAAAAGCACTGAAGAAGATGCCGCAACAAGAGCTTCCAAAGTTTCCCACCGGATCGACGGTACCCTTTCCCTATGAATCTCCTTATCCTCAGCAGACAGCTTTGATGGACACGCTGCTCGAGTGTTTGCAGCAAAAGGATCACGATGATTCAACATGGCGCCAAACCAATGACAGCCATAGCAAGAACAAGAAGAAACCCCGTGCGGCCGTGATGATGTTGGAGTCTCCTACCGGCACTGGCAAGTCTCTATCTTTGGCGTGTAGTGCCATGGCGTGGCTCAAGTACTGCGAACAACGAGATTTGACTGCAGaagaagaatc
QualityScores: 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 38 38 38 40 40 40 39 39 39 40 34 34 34 40 40 40 40 39 26 26 26 26 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 ...

  16. Quality Files .phd .qual >contig00016 length=237 numreads=9 20 3 10 64 14 64 9 64 4 19 64 64 4 64 64 64 64 21 64 37 64 64 64 64 64 64 41 12 64 64 64 64 64 32 64 64 64 64 64 64 64 13 37 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 45 64 64 64 64 64 64 29 64 64 64 64 64 20 64 64 64 64 64 39 64 64 64 64 64 64 64 64 64 64 64 20 64 64 64 64 64 64 64 64 64 64 64 40 64 64 64 64 64 20 64 64 64 64 64 20 64 64 64 64 64 23 64 64 64 64 64 64 64 64 64 64 64 39 64 64 64 64 64 64 16 64 64 64 64 64 64 5 64 64 64 64 64 64 64 64 64 64 64 33 64 64 64 64 64 64 4 64 64 64 64 64 64 64 64 64 64 64 64 29 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 39 64 64 64 64 64 64 48 64 64 64 64 64 64 64 48 64 64 64 50 64 64 64 64 64 64 64 32 64 64 34 64 64 33 64 64 64 48 64 64 64 64 >contig00017 length=161 numreads=9 64 64 64 18 17 64 64 43 20 64 24 41 64 64 30 2 53 64 64 64 64 35 64 64 64 64 64 12 64 64 64 64 31 64 64 28 64 16 64 64 64 64 64 41 64 64 17 64 64 34 25 64 30 64 64 64 64 64 64 64 64 20 64 64 64 64 47 64 64 64 40 64 61 64 64 34 64 64 64 64 64 22 64 64 64 64 64 64 64 64 64 64 64 64 64 58 64 64 64 64 64 64 64 64 64 64 64 58 64 64 64 64 64 64 64 64 64 64 37 43 64 64 52 64 64 64 64 64 64 64 64 64 64 64 60 64 64 49 64 64 64 64 64 64 64 64 20 29 64 64 64 64 64 17 64 21 3 64 21 21 3 BEGIN_SEQUENCE CLS_AGTC_1a73_1_x_C10_FLCN12R_x_A08 BEGIN_COMMENT CHROMAT_FILE: CLS_AGTC_1a73_1_x_C10_FLCN12R_x_A08.ab1 BASECALLER_VERSION: KB 1.2 TRACE_PROCESSOR_VERSION: KB 1.2 QUALITY_LEVELS: 99 TIME: WedDec 07 19:41:26 2011 TRACE_ARRAY_MIN_INDEX: 0 TRACE_ARRAY_MAX_INDEX: 16022 TRIM: -1 -1 -1.000000e+000 TRACE_PEAK_AREA_RATIO: -1.000000e+000 CHEM: term DYE: big END_COMMENT BEGIN_DNA T 3 7 G 3 28 G 4 44 A 6 57 A 5 70 G 3 81 C 4 101

  17. .fastq, .fsq, .fq • Incorporates sequence calls and quality values into a single file: @PXDEO:18:45 ATATATATAAAATATAAAAAGGGTTTTTTTTAAAAAAAATTAATCCAGCAATAATTCCAAATTATTTTGAGGCCGAATCGGATGGGTTATTTTTTTTTTTATAAAAAATTATTTGCAACGAGCCATTATATAACAAA + 9=?>??AAAB@-:0+,000&0:.:;===;=(<<<<677(5151552766>;:>9@8=7:>2=7===>.>=?7=6:<7::<4:<99'0(0*---------%*-*4566)60133,366035665)+0/488443+...

  18. Quality scores in ASCII format SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS..................................................... ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...................... ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII...................... .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ...................... LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL.................................................... !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ | | | | | | 33 59 64 73 104 126 S - Sanger Phred+33, raw reads typically (0, 40) X - Solexa Solexa+64, raw reads typically (-5, 40) I - Illumina 1.3+ Phred+64, raw reads typically (0, 40) J - Illumina 1.5+ Phred+64, raw reads typically (3, 40) with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) (Note: See discussion above). L - Illumina 1.8+ Phred+33, raw reads typically (0, 41)

  19. Why does the encoding start at 33?

  20. File converters • .sfffasta, qual • sffinfo (Newbler tool, www.Roche.com) • sff_extract (bioinf.comav.upv.es/sff_extract/) • .sff .fastq • SFF workbench (www.dnabaser.com/download/) • sff_extract (bioinf.comav.upv.es/sff_extract/) • Sff2fastq (github.com/indraniel/sff2fastq) • .fastq .fasta (&.qual, if desired) • Prinseq-lite.pl or cat file_in.fastq | perl -e '$i=0;while(<>){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}' > file_out.fasta

  21. Quality Metrics • Was the sequencing run successful? • Number of phred20(30) bases • Average read length (@Q20) • How much useable data? • Genome assembly • Total high quality bases • RNAseq/CHIPseq • Total number of map-able reads

  22. Sequence Trimming/Masking/Filtering • Trimming • Barcode & adapter sequences • Poor quality sequence at the starts/ends of reads • Masking • Poor quality sequence in the middles of reads • Filtering • Sequence reads that are shorter than a pre-defined threshold

  23. Quality Trimming/Masking >Sequence1 16 16 21 9 10 13 14 12 8 8 9 16 24 21 19 19 19 25 25 33 35 35 34 34 34 34 34 34 34 40 45 45 56 56 56 51 51 40 45 37 37 37 40 40 40 40 40 40 39 39 39 40 40 40 45 45 45 45 45 45 45 45 45 45 45 45 45 45 45 45 45 51 45 39 39 39 39 39 39 39 39 39 39 39 39 39 39 40 51 51 51 51 51 56 56 56 56 56 56 56 40 35 35 35 35 35 39 40 40 45 45 45 45 45 51 56 40 39 39 39 39 39 45 45 45 45 40 40 40 39 35 35 40 40 40 40 40 40 38 38 38 39 25 23 18 10 8 9 23 31 51 51 45 43 43 43 43 43 43 43 43 43 43 43 43 56 56 56 56 56 56 56 56 43 43 43 43 43 43 45 45 45 51 51 56 51 51 51 51 51 51 56 51 45 43 43 56 56 56 56 56 56 51 51 51 45 45 45 40 40 40 44 42 38 38 40 40 40 51 56 56 56 56 56 46 46 51 51 51 51 56 56 56 56 51 40 45 45 40 40 40 42 42 42 45 45 42 42 42 42 56 42 42 40 40 34 37 33 40 40 40 44 48 48 48 29 29 29 26 32 29 32 32 32 32 33 44 48 56 40 40 40 40 40 40 40 40 40 37 34 34 37 40 40 40 40 37 34 34 48 40 32 28 25 25 25 34 48 48 48 40 40 32 29 24 25 29 40 40 40 40 40 40 33 33 37 40 40 40 43 43 42 42 42 44 44 56 56 56 56 56 40 35 34 33 33 40 40 40 40 40 40 29 29 34 29 29 29 29 40 29 34 25 27 23 23 21 23 18 20 25 25 25 32 32 32 32 29 18 20 14 16 16 17 17 16 22 20 18 25 19 14 16 15 26 27

  24. Masked sequence >Sequence1 CCAGAAACTACGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGATCGTCCGCCAGACTAAAGAAGTCCAAGAGTTGGCTCGCCAAAACGCGCTAAAAACGCAAAAAGCGGCGACCAGTAGANNNNAGGCGAGGCAGGAAGAACAAGCCAACTTTTGGGGTTAACGACTATGTTTTCGTCAAGAAAAAAGGGTTTCCGACGACCGCACCGACGACCAGATTGGATTCACAGTGGACCGGACCATGGCAGATTCTAGAAGAACGAGGATATAGCTATGTTTTGGACGTACCTGAATCGTTTAAAGGAAAAAATTTGTTCCACGCAGACCGCCTCCGCAAAGCCGCAATGGACCCATTACCACAACAGAAAAGAGAGCCGCCTCCGCCAGAAGAGATCAACGCCAGAGTTTGTGGTCGATAAAGTTTTAGCGTCCCGATTATTTGGCCGGAGTAAGATATTGCAATACCAGGTCGCATGGCAAGGATGTGATCCAGACGACACGTGGTACCCGGCTGAAAACTTCAAGAATTCAGCGACAGCCCTTGACGACTTCCACAAGAAGTAC

  25. Sequence header information (Illumina) @M01478:6:000000000-A40C5:1:1101:16859:1439 1:N:0:1 ATCGTTTCGGAGCAAGGCAACTGTNTCAGGCACCATGAAGTTGAGCTATTCTACTGCGCCAACCTTTGCGAGATAAATCGTCNTGCCNTNNTTATCANCGTCAATTGGAANTCAGATGTGCCACCNNAAN + ABBBAABFBBBBGEGGFGGGGGHF#AAFF2AGFGHGHHHHHHFHFFDGFGHHHHGHEGGGGCGGGHFABEEGFFHHEGHEGE#BBFG#?##???FFH#??FEFGHHEHHG#??FFEDGGGFFHFH##??# • Machine name • Run number • Flowcell ID • Flowcell lane • Tile in flowcell • X-coordinate in tile • Y-coordinate in tile • Member of Pair (1/2) • Read filtered? (Y/N) • Control bits on (0 or even number) • Index sequence used

  26. Today’s Exercises • Convert different file formats • Evaluate sequence data quality using FastQC • Trim sequence reads to improve data quality • Re-test trimmed data using FastQC

  27. Tips For a Productive Time • Practice using tab-completion • Make sure you execute all of the steps preceded by check boxes • Tick off/fill-in the check boxes after you have (successfully) completed each command • Do not skip over the text between the check boxes • It provides information designed to aid your understanding of what you are doing • ASK QUESTIONS

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