How to edit a GTF file

Question

[margo]

I am trying to remove columns from a GTF file so I can perform featureCount analysis using the GTF file.

I am only wanting to keep the columns which contain the geneID, chr, start, end and strand data and discard the rest of the columns. I have managed to do this using R by putting the file in a data frame however I am unsure as to how to convert it back to a GTF file from the data frame:

install.packages('BiocManager')
library(BiocManager)
install()
BiocManager::install("Rsubread")
library(Rsubread)


# opening the gtf file as a dataframe 
gtf <- rtracklayer::import('data.gtf')
gtf_df=as.data.frame(gtf)

df = subset(gtf_df, select = -c(seqnames,width,source,type,score,phase,
                                transcript_id,gbkey,gene_biotype,
                                locus_tag,old_locus_tag,protein_id,transl_table,
                                exon_number,gene,Ontology_term,go_component,
                                go_function,go_process,
                                anticodon,transcript_biotype,partial,pseudo,
                                note,db_xref,exception,product,inference))

Is there a way to edit the GTF file using linux? Or a way to make my dataframe from R into a GTF file?

[GenoMax]

featureCounts will understand a properly formatted GTF file, are you not able to use it as is? What you are trying to create is the Simple Annotation Format (SAF ) format file. It will no longer be in GTF format. featureCounts can use SAF format files as well.

Answer 1

[dthorbur]

A GTF is a tab-delimited text file, so you could save the output using the following command:

write.table(df, file = "data.tsv", row.names = FALSE, col.names = FALSE, sep="\t")

However, by removing columns, you will violate the rules of a GTF file which require specific columns. See this description.