gtf需要sort不？

需要特定工具轉(zhuǎn)是因為gtf的起始坐標(biāo)為1

bed的起始坐標(biāo)為0

【1】sort的話：用igv的sort功能

conda install igvtools

?igvtools? sort [options] [inputFile]? [outputFile]

-m??maxRecords The maximum number of records to keep in memory during the?sort. The default value is 500000

【2】轉(zhuǎn)：

gtf2bed < gene.sorted.gtf | head

遇到error：（maybe ensembl）

改為：

awk '{ if ($0 ~ "transcript_id") print $0; else print $0" transcript_id \"\";"; }' Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.sorted.gtf | gtf2bed | head

gtf2bed < gene.sorted.gtf > gene.bed

gtf2bed < gene.sorted.gtf | awk 'BEGIN{FS="\t";OFS="\t"}{print $1,$2,$3,$4,$5,$6}' > gene_6.bed

gtf2bed < gene.sorted.gtf | awk 'BEGIN{FS="\t| |;";OFS="\t"}{print $1,$2,$3,$23,$5,$6}' > gene_6.bed