changing gtf file manually

Question

[zizigolu]

sorry,

in gtf from ensemble there is not any miRNAs but there is in gff3 then I manually change the transcript in gtf to miRNA, finally by this syntax i extracted the read counts

"featureCounts" "-t" "miRNA" "-g" "transcript_id" "-a" "af.gtf" "-o" "2.txt" "2-quality-sorted"

will this change create a miRNA spesific gtf ??? because I need a miRNA annotation which there is not exist for aspergillus fumigatus

> head(gff3[,1:9])

  I CADRE chromosome   X1 X4918979 . ..1 ..2
1 I  JCVI       gene  216      836 .   +   .
2 I  JCVI      miRNA  216      836 .   +   .
3 I  JCVI       exon  216      836 .   +   .
4 I  JCVI        CDS  216      836 .   +   0
5 I  JCVI       gene 3952     4963 .   +   .
6 I  JCVI      miRNA 3952     4963 .   +   .


> gtf <- read.table("Aspergillus_fumigatus.CADRE.32.gtf", header = T, sep = "\t")

> head(gtf[,1:9])

  I JCVI        gene X216 X836 . X. ..1
1 I JCVI  transcript  216  836 .  +   .
2 I JCVI        exon  216  836 .  +   .
3 I JCVI         CDS  216  833 .  +   0
4 I JCVI start_codon  216  218 .  +   0
5 I JCVI  stop_codon  834  836 .  +   0
6 I JCVI        gene 3952 4963 .  +   .

[GenoMax]

I tried to reformat your post but only did it half-way since I am not sure what the rest of the text is.

You just duplicated the entries and changed genes/exons labels to "miRNA"? If miRNA's have not been identified for A. fumigatus then that would require some real experimental/predictive informatics work.

[zizigolu]

thank you. in gff3 as you consider there are chromosome, gene, miRNA, exon and CDS but in gtf there are gene, transcript, exon, CDS, start_codon and stop_codon. I manually changed transcript to miRNA in gtf and used featurecounts syntax -t miRNA supposing I am using miRNA annotation :( :( :(

Answer 1

[komal.rathi]

Why don't you just convert the existing GFF to GTF?

gffread my.gff3 -T -o my.gtf

Source: Convertion Of Gff3 To Gtf

[zizigolu]

thank you. exactly i used this syntax also galaxy but tophat gave me error :( :( :(

[komal.rathi]

Did you try the other solution in the link using rtracklayer::import.gff3? I also wonder if something is wrong with your gff3, which you can validate using: http://genometools.org/cgi-bin/gff3validator.cgi