Question: GFF / Fasta into Trackster
0
gravatar for jasperkoehorst
11 months ago by
Netherlands
jasperkoehorst10 wrote:

Hello,

I am trying to create a small teaching environment and I was hesitating to use either IGV or Galaxy and as I am planning to use galaxy for other steps as well it would be a nice combination.

When loading the fasta file obtained from: https://www.ncbi.nlm.nih.gov/nuccore/J01636 it seems to work ok, cannot visualise the sequence and the 3 reading frames but not sure yet if this is possible?

When loading the gff file I get the following error:

Traceback (most recent call last): File "/galaxy-central/lib/galaxy/datatypes/converters/interval_to_fli.py", line 20, in from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFReaderWrapper, read_unordered_gtf ImportError: No module named galaxy.datatypes.util.gff_util Close

The original docker file that I use as a spin of from the original docker file is located:

https://gitlab.com/wurssb/ibiosystems/tree/master/docker

And the error must have been resolved at https://github.com/galaxyproject/tools-devteam/pull/335 but perhaps I am missing some fundamental binaries due to docker?

The next step would be to visualise bam files with 1x, 10x and 100x read coverage to teach them on the coverage impact

gff trackster • 310 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by jasperkoehorst10

just double checking: the fasta file you want the visualize is the 'genome' sequence? If so, it is best to add the (nucleotide) sequence as a twobit file (see: https://galaxyproject.org/visualization-setup/#optional-but-highly-recommended-get-genome-data )

Regards, Hans-Rudolf

ADD REPLYlink written 11 months ago by Hotz, Hans-Rudolf1.7k

It is indeed a fasta file of ±7kb its an example operon

ADD REPLYlink written 11 months ago by jasperkoehorst10

wrt the gff file: does it work with another (eg smaller, simpler) gff file?

Regards, Hans-Rudolf

ADD REPLYlink written 11 months ago by Hotz, Hans-Rudolf1.7k

The current gff file is only 26 lines but ill try a single gene

ADD REPLYlink written 11 months ago by jasperkoehorst10

well, it looks like, I have just been running into a similar issue as part of upgrading to release v17.01

see: http://dev.list.galaxyproject.org/Convert-BED-to-Feature-Location-Index-breaks-when-preserve-python-environment-legacy-only-tp4670669.html

ADD REPLYlink written 10 months ago by Hotz, Hans-Rudolf1.7k

...and in your case, you probably need to add "CONVERTER_gff_to_fli_0"

I hope this fixes your problem as well. Regards, Hans-Rudolf

ADD REPLYlink written 10 months ago by Hotz, Hans-Rudolf1.7k
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