Hello,
I have used clipplotr many time to plot my iclip data, however, now I get some issues when running the exact same commands I used to run before :
The command I ran :
clipplotr --xlinks "${egfp1}","${egfp2}","${dPLD_egfp1}","${dPLD_egfp2}" --gtf "${gtf}" --region "${coord}" --coverage ${rna_dir}/FBE14/FBE14_NOnorm.${strand}.bw,${rna_dir}/FBE16/FBE16_NOnorm.${strand}.bw,${rna_dir}/FBE18/FBE18_NOnorm.${strand}.bw,${rna_dir}/FBE21/FBE21_NOnorm.${strand}.bw,${rna_dir}/FBE23/FBE23_NOnorm.${strand}.bw,${rna_dir}/FBE25/FBE25_NOnorm.${strand}.bw --coverage_labels 'WT rep1,WT rep2,WT rep3' --coverage_colours '#56EFFC,#42C6EB,#4A9BD9,#F5C1F5,#FF73FF,#BA46D4' --output ${outdir}/${gene_name}_peaks_cov.jpg -l 'WT rep1,WT rep2,DPLD rep1,DPLD rep2' -c 'darkseagreen3,green4,lightpink3, maroon3' --size_y 280 --size_x 350 --ratios '2,0.25,2,0.5'
Examples :
${coord} >> chr3R:14625755:14626614:+
${strand} >> + or -
Thank you,
Hiba
Hello,
I have used clipplotr many time to plot my iclip data, however, now I get some issues when running the exact same commands I used to run before :
The command I ran :
clipplotr --xlinks "${egfp1}","${egfp2}","${dPLD_egfp1}","${dPLD_egfp2}" --gtf "${gtf}" --region "${coord}" --coverage ${rna_dir}/FBE14/FBE14_NOnorm.${strand}.bw,${rna_dir}/FBE16/FBE16_NOnorm.${strand}.bw,${rna_dir}/FBE18/FBE18_NOnorm.${strand}.bw,${rna_dir}/FBE21/FBE21_NOnorm.${strand}.bw,${rna_dir}/FBE23/FBE23_NOnorm.${strand}.bw,${rna_dir}/FBE25/FBE25_NOnorm.${strand}.bw --coverage_labels 'WT rep1,WT rep2,WT rep3' --coverage_colours '#56EFFC,#42C6EB,#4A9BD9,#F5C1F5,#FF73FF,#BA46D4' --output ${outdir}/${gene_name}_peaks_cov.jpg -l 'WT rep1,WT rep2,DPLD rep1,DPLD rep2' -c 'darkseagreen3,green4,lightpink3, maroon3' --size_y 280 --size_x 350 --ratios '2,0.25,2,0.5'Examples :
${coord} >> chr3R:14625755:14626614:+
${strand} >> + or -
Thank you,
Hiba