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Hi,
I'm exploring this wonderful software as a way to get a comprehensive CHM13 TE annotation file for downstream analysis of RNASeq data. The other bits of software I am using requires gtf, rather …
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The spec points here: https://github.com/modENCODE-DCC/validator/blob/master/new_gff_validator.pl
This is 7 year old perl code
The SO wiki has:
http://www.sequenceontology.org/so_wiki/index.php…
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Hello,
I'm wondering if anyone can assist with some issues I'm having re: locus assignment.
Some of my forward primers include ambiguous nucleotides (K, W, R, etc.) and some of the expected STR…
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We need to come up with some stats that we want to display for the gene_models files that are consumed.
Its pretty easy to do counts of field 3 and just report these, but should we do more?
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the number of genes before and after running AGAT longest
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`oe_match("Ireland")` defaults to "https://download.geofabrik.de/europe/iceland-latest.osm.pbf" (note the **iceland** part) as opposed to "https://download.geofabrik.de/europe/ireland-and-northern-ire…
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Hi,
I would like to keep the original GFF features IDs after the merge functional annotations step.
For example I run manually AGAT's agat_sp_manage_functional_annotation.pl and by default origina…
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I tried using the uniprot-sprot proteins as my DB for blast but when I did agat_sp_manage_functional_annotation I got "ERROR P20825 not found among the db! You probably didn't give to me the same fast…
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I know this error has been resolved in other posts, but those solutions did not work for me. This is the output that I am getting:
mkdir: cannot create directory '7321.1.67340.GGTAGC.fastq': File e…
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Hi,
Thank you for implementing AGAT, it's very handy for the analysis of gffs
I was wondering if you could implement a tabular format output option that can enable the generation of a table. Tha…