Using Featurecounts with a custom genome/build

Question: Using Featurecounts with a custom genome/build

6 months ago by

Turkey/Canakkale/Onsekiz Mart University/Department of Biology/Yeast Genetics Lab

I have a trouble with using a data of an experiment about yeast Yarrowia lipolytica. Firstly ı could't get the file from the site www.ebi.ac.uk, so ı have downloaded the file to my pc and the uploaded the file to galaxy. Then I have used succesfully top hat and trimmomatic tools and succesfully loaded fasta and gtf formatted files about Yarrowia lipolytica. But at the end when ı wanted to use the tool "Featurecounts", a warning appears and says "can not use unspecified species, please click the pencil icon and change the species." The obtained file format was bam, but name of species was undefined. I did click this icon but ı couldn't select the species name because there was no loaded data about Yarrowia lipolytica, and also there was no option to load additional files of Yarrowia. So ı could't change or load any information about Yarrowia Could you help me please. Sincerely yours,

Mehmet SOLAK PhD student Yeast Genetics Laboratory/Department of Biology University of 18 MART / CANAKKALE / TURKEY mserafeddinsolak@gmail.com

build featurecounts genome custom rna-seq • 303 views

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modified 6 months ago by tiamaamihyia • 0 • written 6 months ago by mserafeddinsolak • 10

6 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Creating a Custom Genome Build and assigning that to all inputs will allow you to use Featurecounts.

Another user asked about the same issue yesterday and confirmed this also worked for them. The details are here: https://biostar.usegalaxy.org/p/27992/

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson ♦ 25k

6 months ago by

mserafeddinsolak • 10

Turkey/Canakkale/Onsekiz Mart University/Department of Biology/Yeast Genetics Lab

mserafeddinsolak • 10 wrote:

error in featurecounts

Hello again, The problem still continues. I could not finish this work using featurecounts (shared a link about the problem).

Edit: 1) I have changed the version of featurecounts from 1.6.0.3 to 1.6.0.2. Now it seems to be working. Thanks a lot.

Edit: 2) After featurecounts finished the process, ı could not reach the total raw counts, all values are zero in the table. I will check gtf file and try to find another one.

ADD COMMENT • link modified 6 months ago • written 6 months ago by mserafeddinsolak • 10

Check the log from featurecounts to see what data was counted up and what was not (and why).

The most common reason for no counts or very low counts is a genome mismatch between the database used for mapping and the reference annotation GTF dataset.

Sometimes GTF content versus tool settings can contribute to problems -- the GTF must contain the attribute "gene_id" and the type "exon" when using the default settings. Strand is also important -- the strand settings used for mapping should match those set with this tool. These settings and others can be modified to suit your input data/experiment goals under Advanced Options.

FAQs: https://galaxyproject.org/support/#troubleshooting

ADD REPLY • link modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson ♦ 25k

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