This is a test version of Biostars. For the public version, visit https://www.biostars.org.
featureCounts problems with GTF generated by myself

I want to calculate only intron reads in my RNA sequencing. So I generate a GTF file which only contain intron site information. Then save it as gtf. my gtf file

In linux, I use featurecounts like:

featureCounts -T 8 -p 
              -t intron -g gene_name 
              -a intron.gtf -o intron.txt 
               *.sam

Then it shows:

ERROR: no features were loaded in format GTF. The annotation format can be specified by the '-F' option, and the required feature type can be specified by the '-t' option..

I think my GTF has wrong format. So how can I solve it?

featurecounts gtf
• 1,952 views • link
updated by GenoMax GenoMax • written by soda • soda

2 answers

Looking at the data you have it would be best to create a file in Simple Annotation Format (SAF), which featureCounts understands. You can find the example/description of the format in featureCounts manual.

• 0 views • link
written by GenoMax GenoMax

You've made a wrong GTF file. A GTF file should follow a correct format. (You may want to search 'GTF format' in google)

The best way is to download and imitate GTF files from GENCODE.

• 0 views • link
written by maximal_life • maximal_life

Log in to answer this question.

More posts like this