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454 reads runassembly -v –s (remove primer, vector, low quallity region(q13), high coverage(20x)) Contig + Singleton Contig + Singleton Contig + Singleton Contig + Singleton Contig + Singleton Seqclean (short reads remove(100nt)) Contamination remove(microbial i90% l90%) Allele transcripts remove(i99% l-dif 10nt) Alternative splicing remove() Contig + Singleton Homopolymer remove(solexa,solid) Contig + Singleton Scaffold construct ion(cDNA meta-paired) Scaffold construct ion(cDNA meta-paired) Contig + Singleton Contig + Singleton Sequence Extension Unigene Tissues Raw reads Assembled reads Ave len(bp) Median(bp) max_len(bp) Contig num N50(bp) Length(bp) Root 1,008,818 812,252 336 492 5,134 25,799 641 14,725,976 Male bud 324,461 319,860 372 675 25,217 9,885 899 8,673,073 Female bud 2,451,459 2,406,282 336 975 7,537 27,096 1427 31,898,903 Yellow leaf 697,044 504,438 369 479 4,679 17,597 608 9,762,926 Green leaf 1,060,675 339,142 351 572 3,222 2,993 669 1,900,662 Male flower 775,727 764,157 287 493 3,668 14,478 595 8,312,089 Female flower 571,170 567,192 317 512 3,906 14,928 597 8,474,884 Fruit 1,065,993 1,054,098 374 616 7,336 50,784 865 38,109,982 Total 7,955,347 6,767,421 - 967 9,787 55,207 1,532 66,776,885 研究方法和思路 454 Assembly contigs Solexa reads Reads Alignment Bwa sam file Neither pair reads mapping Both pair reads mapping Either pair reads mapping * 研究方法和思路 Neithereither mapping reads Trinity assembly Correct,most extended transcripts Cross-link contigs Genome 454拼接结果 VS cross-link后拼接结果 The statistics of cross-link contigs Cross_link 454 Assembly Total_seq 17782 49147 Total length36265408 Maxmum length 51508 15435 Minimum length 208 80 N50 3305 1234 N90 1041 321 Sum of N 28008 0 1. Identification of genes (De novo transcriptome only) 2. Structure of transcripts: Identification of untranslated region (UTR), boundary of intron,alternative splicing and start codon, etc. 3. Identification of non-coding unit: N
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