Question: Mg-Rast "900" Download File Column Names?
1
gravatar for Dgg32
6.9 years ago by
Dgg3290
Bremen
Dgg3290 wrote:

Hello, community, does anybody have an idea what are the column names of those mg-rast "900" processed files are? Because the description in mg-rast website is outdated. Thank you for everyone!

snippet from "900.abundance.function":

0.0.1    1    1.3e-23    1.3e-23    -23    0    65    65    65    0    78.46    78.46    78.46    0    {d94b489ca8e023488248a6e4b42c09f5}    TrEMBL

1082aa long hypothetical protein    1    9.7e-03    9.7e-03    -3    0    24    24    24    0    79.17    79.17    79.17    0    {d47d136374d6e9809ec6a6516d8ce1a7}    SEED 

10-formyltetrahydrofolate dehydrogenase    8    5.6e-37    2.6e-07    -15.5    11.097    39    138    69.625    34.5085    49.3    71.79    58.1562    7.11562    {0f3319bfe1679ff92a7b1b0ca1bbdc5e,ab7396d0dd2a3c173054dbe17b651dde,4b5158821d0363f73b3f2f2db056d99a}    SwissProt 

10-formyltetrahydrofolate dehydrogenase    2    2.6e-07    2.9e-04    -5.5    2.12132    26    47    36.5    14.8492    55.32    73.08    64.2    12.5582    {4b5158821d0363f73b3f2f2db056d99a,2cae39f3c06a92af5e617caceec788f6}    RefSeq 

10-formyltetrahydrofolate dehydrogenase    4    5.6e-37    2.9e-04    -19    15.6418    26    138    74.25    55.3075    53.62    86.67    67.42    15.4539    {ab7396d0dd2a3c173054dbe17b651dde,cf8ded369c5cf4a5fe4151ee7da9e60f,2cae39f3c06a92af5e617caceec788f6}    GenBank

and snippet from 900.abundance.md5

00003a8575ab2461c908a808ffe2002a    2    1.7e-06    3.8e-04    -5    1.41421    33    42    37.5    6.36396    61.9    63.64    62.77    1.23037

000048fea7b311d6692565d07d372b97    1    4.4e-22    4.4e-22    -22    0    82    82    82    0    65.85    65.85    65.85    0

0000679ceb3fc9c950779468e06329a7    1    1.7e-06    1.7e-06    -6    0    35    35    35    0    68.57    68.57    68.57    0

00008709330856ff934571a2e7e2fa37    2    4.0e-27    3.7e-17    -22    7.07107    63    92    77.5    20.5061    60.32    67.39    63.855    4.99925

0000df506aae07bf400408e5ff692f4c    4    1.2e-13    1.3e-06    -10    3.60555    39    60    51    10.8167    58.33    71.79    64.9767    6.73155
• 1.1k views
ADD COMMENTlink modified 6.9 years ago by Charles Warden7.9k • written 6.9 years ago by Dgg3290
-1
gravatar for Charles Warden
6.9 years ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

You should ignore the .md5 file.

There are lots of potential output tables from MG-RAST.

It looks to me like you have a table of functional enrichment results with the functional category in the first column, p-value in 3rd column, and FDR (?) in 4th column.

I would recommend viewing the results in MG-RAST first. Whenever I have downloaded a table, the format has been the same as was displayed on the website.

Not sure if this is a complete solution, but I did put together a brief tutorial on how to use MG-RAST to analyze metagenomics data:

http://cdwscience.blogspot.com/2013/10/analyze-your-16s-rrna-data-using-mg-rast.html

ADD COMMENTlink written 6.9 years ago by Charles Warden7.9k
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