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RNASeq, gtf file

Hello, I am new to Bioinformatics and I am dealing with a gtf file. I have a gtf file and in this gtf file the column look like following

1   StringTie   transcript  463572  478996  1000    -   .   gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "ENSBTAT00000015319"; ref_gene_id "ENSBTAG00000011528"; ref_gene_name "SMIM11A"; cov "7.464981"; FPKM "8.923761"; TPM "15.880815";
1   StringTie   exon    463572  463746  1000    -   .   gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "ENSBTAT00000015319"; ref_gene_id "ENSBTAG00000011528"; ref_gene_name "SMIM11A"; cov "2.531429";

I want to filter transcript with value FPKM value greater than 2. Please help me

rna-seq sequencing
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updated by Juke34 Juke34 • written by mdfardin374 • mdfardin374

You can do that in Bash or Python for example. Here are the steps :

  • Select "transcript" lines
  • Split by ";"
  • Look for element starting with "FPKM"
  • Once found, compare FPKM value to 2.
  • Keep the line if higher than 2
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written by Bastien Hervé Bastien Hervé

1 answer

You can use agat_sp_filter_feature_by_attribute_value.pl from AGAT

conda create -n agat
conda activate agat
conda --install -c bioconda agat
agat_sp_filter_feature_by_attribute_value.pl --gff input.gff --attribute FPKM --value 2 --test "<" -o result_value_over_or_equal=2.gff
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written by Juke34 Juke34

Hello juke34, I have not used the suggestion given by you, but was curious to know that whether this script will be able to remove all exons associated with transcripts. I am asking this as there is no FPKM information available for exon.

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written by Tm Tm

yes

Removing a level1 (e.g. gene) or level2 (e.g transcript, mRNA) feature will automatically remove all linked subfeatures, and removing all children (e.g: mRNAs of a gene, or exons of an mRNA ) of a feature will automatically remove this feature too.

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written by Juke34 Juke34

Ok got it. Thank you very much for this.

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written by Tm Tm

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