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  • transcriptome assembly got huge contigs

    Hi, I am a beginner of transcriptome assembly. I did a algae transcriptome assembly using spades. I don't understand why I got contigs that is over 25K bp in length. is that possible?
    length. counts of contigs
    100:199 149494
    200:299 709026
    300:399 83948
    400:499 31883
    500:599 16756
    600:699 10221
    700:799 6982
    800:899 4988
    900:999 3538
    1000:1099 2663
    1100:1199 2098
    1200:1299 1627
    1300:1399 1368
    1400:1499 1045
    1500:1599 879
    1600:1699 690
    1700:1799 581
    1800:1899 452
    1900:1999 404
    2000:2099 341
    2100:2199 312
    2200:2299 274
    2300:2399 213
    2400:2499 179
    2500:2599 174
    2600:2699 140
    2700:2799 132
    2800:2899 132
    2900:2999 96
    3000:3099 93
    3100:3199 83
    3200:3299 91
    3300:3399 85
    3400:3499 73
    3500:3599 75
    3600:3699 65
    3700:3799 87
    3800:3899 69
    3900:3999 67
    4000:4099 55
    4100:4199 48
    4200:4299 49
    4300:4399 48
    4400:4499 56
    4500:4599 61
    4600:4699 47
    4700:4799 53
    4800:4899 49
    4900:4999 44
    5000:5099 42
    5100:5199 30
    5200:5299 46
    5300:5399 37
    5400:5499 41
    5500:5599 32
    5600:5699 27
    5700:5799 35
    5800:5899 30
    5900:5999 44
    6000:6099 34
    6100:6199 35
    6200:6299 22
    6300:6399 25
    6400:6499 28
    6500:6599 24
    6600:6699 39
    6700:6799 33
    6800:6899 28
    6900:6999 28
    7000:7099 22
    7100:7199 22
    7200:7299 24
    7300:7399 19
    7400:7499 30
    7500:7599 36
    7600:7699 27
    7700:7799 14
    7800:7899 16
    7900:7999 23
    8000:8099 16
    8100:8199 21
    8200:8299 14
    8300:8399 17
    8400:8499 17
    8500:8599 14
    8600:8699 18
    8700:8799 13
    8800:8899 11
    8900:8999 12
    9000:9099 12
    9100:9199 10
    9200:9299 8
    9300:9399 11
    9400:9499 14
    9500:9599 13
    9600:9699 16
    9700:9799 6
    9800:9899 9
    9900:9999 11
    10000:10099 8
    10100:10199 5
    10200:10299 10
    10300:10399 8
    10400:10499 7
    10500:10599 4
    10600:10699 6
    10700:10799 5
    10800:10899 4
    10900:10999 7
    11000:11099 6
    11100:11199 3
    11200:11299 3
    11300:11399 6
    11400:11499 7
    11500:11599 8
    11600:11699 6
    11700:11799 13
    11800:11899 6
    11900:11999 4
    12000:12099 4
    12100:12199 7
    12200:12299 4
    12300:12399 4
    12400:12499 5
    12500:12599 4
    12600:12699 6
    12700:12799 8
    12800:12899 10
    12900:12999 3
    13000:13099 8
    13100:13199 3
    13200:13299 6
    13300:13399 1
    13400:13499 4
    13500:13599 6
    13600:13699 4
    13700:13799 4
    13800:13899 3
    13900:13999 1
    14000:14099 3
    14100:14199 3
    14200:14299 3
    14300:14399 3
    14400:14499 2
    14500:14599 3
    14600:14699 3
    14700:14799 2
    14800:14899 1
    14900:14999 1
    15000:15099 2
    15100:15199 3
    15200:15299 2
    15300:15399 2
    15400:15499 1
    15500:15599 2
    15600:15699 1
    15700:15799 2
    15800:15899 2
    15900:15999 2
    16000:16099 3
    16100:16199 2
    16200:16299 1
    16300:16399 1
    16400:16499 2
    16500:16599 4
    16600:16699 1
    16700:16799 1
    16800:16899 2
    17000:17099 1
    17300:17399 2
    17400:17499 1
    17500:17599 1
    17700:17799 1
    17800:17899 1
    17900:17999 3
    18200:18299 1
    18300:18399 1
    18500:18599 1
    18700:18799 1
    18800:18899 1
    18900:18999 1
    19100:19199 1
    19200:19299 1
    19300:19399 1
    19500:19599 2
    19800:19899 1
    19900:19999 1
    20100:20199 1
    20300:20399 2
    20500:20599 1
    20900:20999 1
    21100:21199 1
    21500:21599 1
    21700:21799 2
    21900:21999 1
    22000:22099 1
    23000:23099 1
    23100:23199 1
    24600:24699 1
    25200:25299 1
    25500:25599 1
    26500:26599 1
    26900:26999 1
    27800:27899 1
    28800:28899 1
    31500:31599 1
    38800:38899 1

    Total length of sequence: 298114914 bp
    Total number of sequences: 1033416
    N25 stats: 25% of total sequence length is contained in the 76269 sequences >= 437 bp
    N50 stats: 50% of total sequence length is contained in the 327373 sequences >= 238 bp
    N75 stats: 75% of total sequence length is contained in the 657535 sequences >= 214 bp
    Total GC count: 137442543 bp
    GC %: 46.10 %

  • #2
    Unlikely that they derive from RNA. My guess would be that if you took a few kb of sequence from the largest contig and did a blastn to nt at genbank you would get a hit to chloroplast. Speculation on my part, of course...

    --
    Phillip

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