Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

      Latest Articles

      Collapse

      • seqadmin
        Advanced Tools Transforming the Field of Cytogenomics
        by seqadmin


        At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...
        09-26-2023, 06:26 AM
      • seqadmin
        How RNA-Seq is Transforming Cancer Studies
        by seqadmin



        Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...
        09-07-2023, 11:15 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 09:38 AM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-27-2023, 06:57 AM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-26-2023, 07:53 AM
      1 response
      23 views
      0 likes
      Last Post seed_phrase_metal_storage  
      Started by seqadmin, 09-25-2023, 07:42 AM
      0 responses
      17 views
      0 likes
      Last Post seqadmin  
      Working...
      X