Question: FeatureCounts from GUI galaxy
0
gravatar for andrewzlobin
5 months ago by
andrewzlobin20
andrewzlobin20 wrote:

I ran featurecounts from Galaxy GUI – it didn’t recognized genomic annotation UCSC from history. By no means! It runs on its own build in hg38, and it gave me (in table) not uc.3458…. ID but just numbers, which I cannot convert to Gene Symbols. What's the problem? How do you do it? Any suggestion?

Thanks

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ADD COMMENTlink modified 3 months ago • written 5 months ago by andrewzlobin20
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

With FeatureCounts, when the option for Gene annotation file is set to "in your history", any datasets with a GTF or GFF datatype in the same history will be selectable as input. Maybe you need to change this option or the annotation dataset datatype assignment? https://galaxyproject.org/support/#getting-inputs-right

The FeatureCounts built-in annotations are described on the tool form (databases supported: hg38, hg19, mm10 and mm9) and in this post: https://biostar.usegalaxy.org/p/27461/

How to convert identifiers or add in gene symbols can vary by the tools available/installed on the Galaxy server you are working at. If at https://usegalaxy.org, the tool UniProt ID mapping and retrieval can convert IDs. Or you can upload any tabular mapping file to Galaxy that contains the IDs in your output and the IDs you want to convert to and merge the two with the tool Join two files or Join two Datasets side by side on a specified field.

Examples of joining data are in the Galaxy 101 tutorial: https://galaxyproject.org/learn/

All Support FAQs: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k

Update

The Featurecounts tool now requires that the database metadata assignment is made to both the BAM and GTF inputs (when sourced from the history).

Please see this post for full details: https://biostar.usegalaxy.org/p/24154/#28027

Thanks! Jen, Galaxy team

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson25k
0
gravatar for andrewzlobin
3 months ago by
andrewzlobin20
andrewzlobin20 wrote:

Thanks a lot, it's great!

ADD COMMENTlink written 3 months ago by andrewzlobin20
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