I would suggest to useagat_convert_sp_gff2gtf.plfromAGATbecause you loose information withgffread. e.g here a gff example: ##gff-version 3scaffold625 maker gene 337818 343277 . + . ID=CLUHARG00000005458;Name=TUBB3_2scaffold625 maker transcript 337818 343277 . + . ID=CLUHART00000008717;Par...
On the other hand I do realize that gffread still has some shortcomings when it comes to GFF3 output and I am willing to work on improving this GFF3 output (but not GTF). In my opinion GTF is (or should be) obsolete and should not be used (even adding a "transcript" feature line ...
#GFF3_to_GTF.pl #Usage: GFF3_to_GTF.pl -options <filename> usestrict; useGetopt::Long; usecarp; my$file;#File name of input (GFF3 format) my$file_root;#Root of file name (i.e. name minus .gff3) my$outfile;#Output file name (root.gtf) ...
1.gff3_to_bed Approadch 1: 利用TransDecoder的gff3_file_to_bed.pl脚本完成(conda 安装TransDecoder) gff3_file_to_bed.pl/public/home/qtxu/rice_anotation/Rice_annotation/Tige7.0.gff3>Tigr_MSU_7_raw.bed#format the bed files!sed's/;LOC\S*\t/\t/g'Tigr_MSU_7_raw.bed|sed's/ID=//g...
gfftobed 转换GFF3 / GTF到BED 该程序采用GFF3或GTF(基于1)格式的输入基因组注释,并将特定特征转换为6列BED格式(基于0),同时保留注释文件属性列的任何所需字段。 当需要围绕特定特征和唯一ID的基因组间隔时,此功能很有用。 它还可以在每个功能周围添加一个窗口。 处
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The gene_id is only achieved when using refTables (a format specified in UCSC's web browser), you can see a more elaborate answer here Obtaining Ucsc Tables Via Ftp And Converting Them To Proper Gff3 Via Genepredtogtf?. Other options Other scripts/tools That DO NOT produce a compl...
impact: the missing ; fails some tools in the genome annotation tutorials -- Workaround for end-users Run the toolText transformation with sedon your GTF file This expression is one way to fix the problem:s/(transcript[^_].+$)/\1;/ ...
gt_gtf_to_gff3_test_inconsistent_strand2.gtf Go to file Cannot retrieve contributors at this time 52 lines (52 sloc) 6.68 KB Raw Blame chr1 unknown exon 11874 12227 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018"; tss_id "TSS14844"; chr1 unk...