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wu-lab-egio / EGIO

Exon Group Ideogram based detection of Orthologous exons and Orthologous isoforms
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Questions about input file templates #5

Closed Tang-pro closed 4 months ago

Tang-pro commented 6 months ago

Hi, @wu-lab-egio

Very useful software, but this software is not generally friendly and convenient, here I encountered some errors `/usr/bin/ld.gold: --push-state: unknown option /usr/bin/ld.gold: use the --help option for usage information collect2: error: ld returned 1 exit status Traceback (most recent call last):

IndexError: list index out of range BLAST options error: File extrainfo/Ghir.exonfasta does not exist Command line argument error: Argument "query". File is not accessible: extrainfo/Gbar.exonfasta' Command line argument error: Argument "query". File is not accessible:extrainfo/Ghir.exonfasta'`

Can you provide the template of the input file directly here? Best !

wu-lab-egio commented 5 months ago

Hi,

I am sorry to miss the email. To find the input file format, please refer to the example files at https://github.com/wu-lab-egio/EGIO_example_source. When running the sample, please unzip the xx.gtf.zip files first.

When preparing your input file, please make sure that the gtf and DNA fasta files are from the same genome annotation. Some genes may be kicked out or newly-predicted in the new annotation version, such as Ensembl release v102 vs release v99.