Question: getting miRBase microRNAs gff Aspergillus fumigatus
0
gravatar for F
3.0 years ago by
F3.4k
Iran
F3.4k wrote:

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

mirna rna-seq • 801 views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by F3.4k
1
gravatar for F
3.0 years ago by
F3.4k
Iran
F3.4k wrote:

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?

ADD COMMENTlink written 3.0 years ago by F3.4k
2

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 ?

ADD REPLYlink written 3.0 years ago by Prasad1.6k

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???

ADD REPLYlink written 3.0 years ago by F3.4k

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Prasad1.6k

thank you

may please tell me what should this code in R

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

ADD REPLYlink written 3.0 years ago by F3.4k
1
gravatar for robm9119
3.0 years ago by
robm9119150
United States
robm9119150 wrote:

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

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

ADD COMMENTlink written 3.0 years ago by robm9119150

yes I know then what can I do??

ADD REPLYlink written 3.0 years ago by F3.4k
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