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 Because the description in mg-rast website is outdated.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
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Dgg32
1 answer
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
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