Question: Help with an simple workflow (annotation)?
0
gravatar for vebaev
3 months ago by
vebaev130
vebaev130 wrote:

Dear all, I need a recommendation about what tools to use in a workflow for annotation of sequences. Basically, I have contigs I have to map and annotate in a genome and get results each contig from which region comes (GFF on the genome is provided also along fasta)?

annotation galaxy local • 187 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by vebaev130
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Galaxy tutorials: https://galaxyproject.org/learn/

Public Galaxy sites, some of which are Domain-specific and include alternative/more tools than the primary public servers/mirrors: https://usegalaxy.org, https://usegalaxy.eu, https://usegalaxy.org.au >> https://galaxyproject.org/public-galaxy-servers/

It is not quite clear which analysis you are attempting, so I cannot recommend a specific tutorial or public Domain-specific server.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k

As my thoughts are cleared, I need a way to convert a table blast result to GFF so I can intersect it with the genome GFF for annotation purposes? Is there such tool?

ADD REPLYlink written 3 months ago by vebaev130

Table Blast results are almost in the interval format. You will need to subtract 1 base from the start coordinates to make it fully match interval format. Use the tool Text Manipulation > Compute to adjust the coordinate and optionally the tool Cut to rearrange/pick the final columns to retain.

Obtain your genome annotation in bed or interval format and load that to Galaxy.

Then the two interval datasets can be compared/merged/joined/etc with tools in the groups: Operate on Genomic Intervals; Text Manipulation; Datamash; Convert Formats; Filter and Sort; Join, Subtract and Group

For a short example of comparing two annotation datasets, please see the Galaxy 101 tutorial here https://galaxyproject.org/learn/

If you could output XML from BLAST, the tool Parse blast XML output can convert it to tabular format (slightly different formatting than outputting tabular directly, see the tool form). This output would need the same start coordinate adjustments to match interval format specifications.

FAQs:

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k
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