[Gmod-help] convert GFF files

[Petrin, Raul]

Hi

I know that you got a lot of email regarding Convert GFF to GFF3, but I
was reading but I didn't found this full information.

I have one file that I would like to convert to GFF3. Example.

 

##gff-version 3

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
11                 61                 1406.89          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000011;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
29                 87                 1286.67          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000029;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
62                 118               1244.11          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000062;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
87                 142               1321.22          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000087;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
114               168               1431.89          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000114;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
151               207               1098.56          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000151;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
179               241               1658.33          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000179;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
197               255               1747.22          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000197;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
225               282               1359.78          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000225;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
253               310               2027.00          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000253;count=1

SCAFFOLD_1000                  NimbleScan     data_Day1_532:BLOCK1
291               350               1631.78          .
.
seq_id=SCAFFOLD_1000:1-3586;probe_id=SCAFFOLD_1000FS000000291;count=1

 

Which tools can I use to convert?

Thank you so much.

 

Raul Petrin

2121 ML - 384-1015

University of Iowa

 




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