Question: Glimmer 3 multi-extract input problem
0
gravatar for thepunkoklos
3.4 years ago by
United States
thepunkoklos0 wrote:

The thing is I have a multi FASTA file and I was hoping to extract the gene coding regions with Glimmer multi-extract. I have already used the glimmer3 script and got two files: a .predict and a .detail. Now, when I try to use multi-extract it just gives me an error. Multi-extract asks me for this:

USAGE:  multi-extract [options] <sequence-file> <coords>

Read multi-fasta-format <sequence-file> and extract from it the
subsequences specified by <coords>.  By default, <coords>
is the name of a file containing lines of the form
  <id>  <tag>  <start>  <stop>  [<frame>] ...
<id> is the identifier for the subsequence
<tag> is the tag of the sequence in <sequence-file> from which
to extract the entry

Now, although the glimmer3 package itself doesn't tell you from where you're supposed to get your <coords> file I assume it is from the .predict file (though some biolinux website suggested that the long-orfs output would do. In any case long-orfs doesn't seem to work with multi fasta as it only extracts the orfs from the first contig in my file.). But then.... the .predict file doesn't have the right structure, for a start it doesn't even include an <id> column, it's something like this:

>contig-7
orf00002     1741      461 
orf00003     3381     1747 
>Wcontig-7000023
>Wcontig-11112
orf00001      426     2648 
orf00002     2710     4581 
orf00003     4569     5480 
orf00004     6990     6133 
orf00006     9180     7108 
orf00007    10201     9209 
orf00008    11663    10203 
orf00009    12489    11680 
orf00010    13153    12473 
orf00011    14382    13225 
orf00013    14715    15968 
orf00014    19868    16410 
>Wcontig-1674000002
orf00001     2995      637 
orf00002     2497     1166 
orf00003     2984     2529

 

Does anybody know if I'm doing something terribly wrong or do I have to apply some commands to the file in order for it to meet multi-extract rules?

glimmer extract • 1.7k views
ADD COMMENTlink modified 2.6 years ago by linheyu111710 • written 3.4 years ago by thepunkoklos0
0
gravatar for linheyu1117
2.6 years ago by
linheyu111710
China
linheyu111710 wrote:

hi, have you solved this problem? I met the same problem as yours.

What do you do next?

ADD COMMENTlink written 2.6 years ago by linheyu111710
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