getting miRBase microRNAs gff Aspergillus fumigatus

Question

[zizigolu]

hi,

I am performing differential expression of pathogen fungi Aspergillus fumigatus miRNAs in response to human blood infection.

first I trimmed adapters, then mapped trimmed fastq against whole genome fasta of Aspergillus fumigatus by bowtie2 now I am going to extract read count by htseq-count then i need miRBase microRNAs gff for Aspergillus fumigatus but after too much googling I did not find. do you know what can I do please? where I can find miRBase microRNAs gff or Aspergillus fumigatus or can I Aspergillus fumigatus gf3 from enseble neglecting I am working with miRNA????

thank you

Answer 1

[zizigolu]

I should download Aspergillus_fumigatus.CADRE.32.gff3 from ensembl but it contains not only miRNA but also CDS and exons then how I can extract miRNA from this file?

[Prasad]

You want to extract just miRNA coordinates

awk -F "\t"  '$3 == "miRNA"{print}' gff >out_miRNA

But the strange thing is biotype of these miRNA are protein coding. miRNAs are non coding right ?

[zizigolu]

thank you I am performing DE for miRNAs then after providing bam file by bowtie2 I need a gff to extract read counts which should be unique miRNAs, am I wrong please???

[Prasad]

then no need to seperate miRNA coordinates. you can use complete gff to get the readcount using stringtie(faster than latter) or cufflinks. each instances of miRNA in the gff are unique

[zizigolu]

thank you

may please tell me what should this code in R

awk -F "\t" '$3 == "miRNA"{print}' gff >out_miRNA

Answer 2

[robm9119]

I don't think Aspergillus fumigatus is in the miRBase database:

ftp://mirbase.org/pub/mirbase/CURRENT/genomes/

[zizigolu]

yes I know then what can I do??