How to convert a text file into gtf file?
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2.3 years ago

I am facing a problem while running feature counts as my input reference file is in text format. I would like to know a way to convert this file into gtf.

>hsa_piR_000001|gb|DQ569913|Homo sapiens:21:43519790:43519815:Plus
AAACAAACCUGACUUUGUGGGGGCGC
>hsa_piR_000002|gb|DQ569914|Homo sapiens:15:49361981:49362009:Minus
AAACAAAGAAACAGGUGGUGAGAAUGUGU
>hsa_piR_000003|gb|DQ569915|Homo sapiens:19:39999145:39999173:Minus
AAACAGAUGUGCUCAAGCUGAGUGGUCCA
>hsa_piR_000004|gb|DQ569917|Homo sapiens:2:231979486:231979511:Minus
AAACAGUGGUUACAGGGGGCUCAGAU
>hsa_piR_000005|gb|DQ569918|Homo sapiens:3:199288152:199288178:Minus
AAACAUUGAGGAUGUCUACGGCAACAC
>hsa_piR_000006|gb|DQ569921|Homo sapiens:11:13587875:13587903:Plus
AAACCGAAUAAAGUCUUCAUCUGAUGCUC
>hsa_piR_000007|gb|DQ569922|Homo sapiens:12:131188624:131188651:Minus
AAACCUACAUCCACACAGAAACGUACAC
>hsa_piR_000008|gb|DQ569923|Homo sapiens:17:362636:362661:Plus
AAACGAGGUAAUGAUCCUGGAGCCUA


This is the input text file.

RNA-Seq • 1.1k views
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A little bit more info would be appreciated, but maybe you can do it re-ordering the columns. See more abour the GTF format Here