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  • Velvet assembly

    I have run velvet for hash length 31 and 51 without setting any parameters.Then I calculated exp_cov and cov_cutoff using given perl script (velvet-estimate-exp_cov.pl).

    For the hash 31, I found velvetg parameters exp_cov and cov_cutoff to be 1 and 0. I expected these values to go further down for hash 51 (since higher K-mer gives lower coverage). But surprisingly, it was 17 and 0. I have attached the outputs of the perl script for two hash lengths.

    Could anyone explain this?

    Expected coverage

    1 | 19 |
    2 | 16 |
    3 | 3 |
    4 | 36 | *
    5 | 66 | **
    6 | 69 | **
    7 | 108 | ****
    8 | 119 | ****
    9 | 169 | ******
    10 | 196 | ********
    11 | 261 | **********
    12 | 327 | *************
    13 | 503 | ********************
    14 | 635 | **************************
    15 | 970 | ***************************************
    16 | 1210 | *************************************************
    17 | 1459 | ************************************************************
    18 | 1330 | ******************************************************
    19 | 951 | ***************************************
    20 | 545 | **********************
    21 | 286 | ***********
    22 | 160 | ******
    23 | 84 | ***
    24 | 48 | *
    25 | 36 | *
    26 | 20 |
    27 | 12 |
    28 | 10 |
    29 | 11 |
    30 | 10 |
    31 | 8 |
    32 | 6 |
    33 | 8 |
    34 | 3 |
    35 | 3 |
    36 | 2 |
    37 | 2 |
    38 | 3 |
    39 | 4 |
    40 | 1 |
    43 | 1 |
    44 | 2 |
    45 | 1 |
    47 | 1 |
    48 | 1 |
    49 | 2 |
    50 | 1 |
    51 | 1 |
    53 | 1 |
    55 | 1 |
    61 | 2 |
    66 | 1 |
    67 | 1 |
    74 | 1 |
    77 | 2 |
    85 | 1 |
    86 | 2 |
    87 | 1 |
    93 | 1 |
    95 | 2 |
    105 | 2 |
    114 | 1 |
    127 | 1 |
    138 | 1 |
    139 | 1 |
    142 | 1 |
    144 | 1 |
    145 | 1 |
    147 | 1 |
    157 | 1 |
    169 | 1 |
    173 | 1 |
    178 | 1 |
    185 | 1 |
    219 | 1 |
    236 | 1 |
    263 | 1 |
    273 | 1 |
    278 | 1 |
    291 | 1 |
    312 | 1 |
    313 | 1 |
    316 | 1 |
    317 | 1 |
    324 | 1 |
    329 | 1 |
    332 | 1 |
    347 | 1 |
    350 | 1 |
    366 | 1 |
    369 | 1 |
    371 | 1 |
    399 | 1 |
    411 | 1 |
    430 | 1 |
    433 | 1 |
    455 | 1 |
    492 | 1 |
    502 | 1 |
    506 | 1 |
    522 | 1 |
    546 | 1 |
    561 | 1 |
    706 | 1 |
    775 | 1 |
    Predicted expected coverage: 17
    velvetg parameters: -exp_cov 17 -cov_cutoff 0

    Observed results

    1 | 2773 | ************************************************************
    2 | 1740 | *************************************
    3 | 374 | ********
    4 | 41 |
    5 | 14 |
    6 | 5 |
    7 | 4 |
    8 | 3 |
    9 | 8 |
    10 | 12 |
    11 | 17 |
    12 | 19 |
    13 | 28 |
    14 | 30 |
    15 | 54 | *
    16 | 63 | *
    17 | 83 | *
    18 | 110 | **
    19 | 154 | ***
    20 | 174 | ***
    21 | 233 | *****
    22 | 260 | *****
    23 | 339 | *******
    24 | 400 | ********
    25 | 493 | **********
    26 | 595 | ************
    27 | 681 | **************
    28 | 835 | ******************
    29 | 897 | *******************
    30 | 1148 | ************************
    31 | 1234 | **************************
    32 | 1449 | *******************************
    33 | 1500 | ********************************
    34 | 1661 | ***********************************
    35 | 1839 | ***************************************
    36 | 1972 | ******************************************
    37 | 2150 | **********************************************
    38 | 2208 | ***********************************************
    39 | 2235 | ************************************************
    40 | 2469 | *****************************************************
    41 | 2433 | ****************************************************
    42 | 2528 | ******************************************************
    43 | 2467 | *****************************************************
    44 | 2462 | *****************************************************
    45 | 2387 | ***************************************************
    46 | 2403 | ***************************************************
    47 | 2281 | *************************************************
    48 | 2206 | ***********************************************
    49 | 2101 | *********************************************
    50 | 1981 | ******************************************
    51 | 1866 | ****************************************
    52 | 1661 | ***********************************
    53 | 1640 | ***********************************
    54 | 1558 | *********************************
    55 | 1402 | ******************************
    56 | 1328 | ****************************
    57 | 1154 | ************************
    58 | 1093 | ***********************
    59 | 1016 | *********************
    60 | 907 | *******************
    61 | 842 | ******************
    62 | 789 | *****************
    63 | 730 | ***************
    64 | 603 | *************
    65 | 631 | *************
    66 | 527 | ***********
    67 | 499 | **********
    68 | 437 | *********
    69 | 353 | *******
    70 | 333 | *******
    71 | 356 | *******
    72 | 280 | ******
    73 | 261 | *****
    74 | 249 | *****
    75 | 255 | *****
    76 | 215 | ****
    77 | 172 | ***
    78 | 164 | ***
    79 | 137 | **
    80 | 143 | ***
    81 | 132 | **
    82 | 119 | **
    83 | 118 | **
    84 | 79 | *
    85 | 74 | *
    86 | 67 | *
    87 | 84 | *
    88 | 67 | *
    89 | 64 | *
    90 | 46 |
    91 | 59 | *
    92 | 44 |
    93 | 47 | *
    94 | 43 |
    95 | 24 |
    96 | 29 |
    97 | 25 |
    98 | 26 |
    99 | 20 |
    100 | 20 |
    101 | 12 |
    102 | 16 |
    103 | 12 |
    104 | 11 |
    105 | 11 |
    106 | 13 |
    107 | 12 |
    108 | 7 |
    109 | 6 |
    110 | 6 |
    111 | 4 |
    112 | 7 |
    113 | 10 |
    114 | 6 |
    115 | 2 |
    116 | 3 |
    117 | 2 |
    119 | 1 |
    120 | 5 |
    121 | 3 |
    122 | 2 |
    123 | 4 |
    125 | 3 |
    126 | 3 |
    127 | 2 |
    128 | 1 |
    129 | 1 |
    130 | 1 |
    134 | 2 |
    135 | 1 |
    136 | 3 |
    137 | 2 |
    141 | 3 |
    142 | 1 |
    146 | 3 |
    147 | 1 |
    148 | 1 |
    150 | 2 |
    151 | 3 |
    153 | 1 |
    158 | 1 |
    166 | 1 |
    170 | 1 |
    175 | 1 |
    179 | 1 |
    181 | 1 |
    185 | 1 |
    186 | 1 |
    190 | 1 |
    196 | 2 |
    201 | 1 |
    206 | 2 |
    207 | 1 |
    209 | 1 |
    217 | 1 |
    221 | 1 |
    222 | 1 |
    227 | 1 |
    229 | 1 |
    237 | 1 |
    241 | 1 |
    243 | 1 |
    258 | 1 |
    261 | 1 |
    262 | 1 |
    267 | 1 |
    269 | 1 |
    272 | 1 |
    273 | 1 |
    282 | 1 |
    287 | 1 |
    288 | 1 |
    290 | 1 |
    294 | 1 |
    295 | 1 |
    299 | 1 |
    303 | 1 |
    310 | 1 |
    318 | 1 |
    321 | 1 |
    324 | 1 |
    325 | 1 |
    329 | 1 |
    330 | 2 |
    332 | 1 |
    334 | 1 |
    340 | 1 |
    341 | 2 |
    347 | 1 |
    359 | 1 |
    360 | 1 |
    361 | 1 |
    363 | 1 |
    368 | 1 |
    373 | 1 |
    376 | 1 |
    380 | 1 |
    404 | 1 |
    411 | 1 |
    422 | 1 |
    434 | 1 |
    435 | 1 |
    444 | 1 |
    451 | 2 |
    463 | 1 |
    464 | 1 |
    465 | 1 |
    473 | 1 |
    500 | 1 |
    510 | 1 |
    514 | 1 |
    516 | 1 |
    524 | 1 |
    551 | 1 |
    558 | 1 |
    561 | 1 |
    562 | 1 |
    589 | 1 |
    610 | 1 |
    637 | 1 |
    645 | 1 |
    674 | 1 |
    716 | 1 |
    718 | 1 |
    741 | 1 |
    775 | 1 |
    777 | 1 |
    778 | 1 |
    787 | 1 |
    797 | 1 |
    806 | 1 |
    826 | 1 |
    861 | 1 |
    862 | 1 |
    880 | 1 |
    937 | 1 |
    949 | 1 |
    962 | 1 |
    965 | 1 |
    971 | 1 |
    979 | 1 |
    983 | 1 |
    1003 | 1 |
    1036 | 1 |
    1064 | 1 |
    1087 | 1 |
    1100 | 1 |
    1287 | 1 |
    1342 | 1 |
    1365 | 1 |
    1408 | 1 |
    1433 | 1 |
    1512 | 1 |
    1649 | 1 |
    Predicted expected coverage: 1
    velvetg parameters: -exp_cov 1 -cov_cutoff 0

  • #2
    It looks like the perl script simply selects the mode of the k-mer frequency histogram: 1 and 17 are the most frequent values in the two histograms you show. The histogram for k=31 looks as expected to me (many low-frequency k-mers which represent k-mers with sequencing errors then a proper distribution of k-mers around 40-45X). The k=51 histogram does not look right. I would guess the k=51 assembly failed for some reason - probably not enough coverage to support that high kmer length.

    I suggest trying the VelvetOptimiser script which is included with velvet.
    Last edited by jts; 12-12-2010, 09:03 AM.

    Comment


    • #3
      Thanks a lot jts. I will try velvetOptimiser.

      Comment

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