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This is regarding a de novo genome of a plant that was assembled lately. I used AGAT's feature extraction tool, to get the gene models predicted by AUGUSTUS. The repeat-masked genome is of size 2.6gb, and the fasta file resulted from AGAT's feature extraction file was ~600Mb, comprising 500K gene models. The following command was used for AGAT's feature extraction. I just like to know if this is the right command that was supposed to be used as my output file contains way too many short sequences.
Have you checked the help? https://nbisweden.github.io/AGAT/tools/agat_sp_extract_sequences/#briefly-in-pictures
I guess the --split is useless.
Then if you want to extract everything from the start of the gene to the end of (So it contains UTR+exon+intron) -t gene is correct.
If you want to check what is in your file before to use agat_sp_extract_sequences.pl to be sure you had 500K gene as input in the GFF use agat_sq_stat_basic.pl prior your analyse.
This is regarding a de novo genome of a plant that was assembled lately. I used AGAT's feature extraction tool, to get the gene models predicted by AUGUSTUS. The repeat-masked genome is of size 2.6gb, and the fasta file resulted from AGAT's feature extraction file was ~600Mb, comprising 500K gene models. The following command was used for AGAT's feature extraction. I just like to know if this is the right command that was supposed to be used as my output file contains way too many short sequences.
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