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Question: Confusion regarding gffread tool in Galaxy
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gravatar for prasanthbds10
3 months ago by
prasanthbds10 • 0
prasanthbds10 • 0 wrote:

Dear All,

I am new to analysis of RNA sequencing data. I am looking to map small RNA sequencing data with a gff3 file I downloaded from miRBase. Now, I need to convert the .gff3 file to gtf file for usage in mapping tools. I went through the Biostars looking for older posts but I still could not understand how to properly convert the .gff3 file and I am still confused on the filters that the tool has, for the conversion of .gff3 file to gtf file. Can anyone please guide me on the usage of gffread tool in Galaxy?

Thanking you in advance, Prasanth
rna-seq gff3 galaxy gffread gtf • 165 views
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modified 3 months ago by Jennifer Hillman Jackson ♦ 25k • written 3 months ago by prasanthbds10 • 0
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gravatar for Jennifer Hillman Jackson
3 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool will transform GFF3 to GTF format using all default parameters with the exception of the option "Feature File Output". Choose GTF and supply a track name (a single alphanumeric "word" is best).

The other parameters are primarily filters that can be applied (or skipped). These are the same as when the tool is used line-command and/or the option is explained on the tool form. http://ccb.jhu.edu/software/stringtie/gff.shtml

If you need more help to better understand a specific parameter, which one?

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3 months ago by Jennifer Hillman Jackson ♦ 25k
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