Loading hic_generation.sh +25 −24 Original line number Diff line number Diff line Loading @@ -104,33 +104,34 @@ do \nexport _JAVA_OPTIONS=\"-Xmx60g -Xms60g\"\ \n\ \nif [ ! -e $stat_m ];then\ \ndups=\$(\\\ \n\t$samtools_cmd \\\ \n\t\tview \\\ \n\t\t\t-c \\\ \n\t\t\t-f 1089 \\\ \n\t\t\t-F 256 \\\ \n\t\t\t-@ $thread_str \\\ \n\t\t\t$merged_dedup_bam\\\ \n) \ \n\ \ncat \\\ \n\t${split_dir}/*.res.txt | \\\ \n$awk_cmd \\\ \n\t-v dups=\$dups \\\ \n\t-v ligation=$ligation \\\ \n\t-f ${common_dir}/stats_sub.awk \\\ \n> $stat_txt \ \n\tdups=\$(\\\ \n\t\t$samtools_cmd \\\ \n\t\t\tview \\\ \n\t\t\t\t-c \\\ \n\t\t\t\t-f 1089 \\\ \n\t\t\t\t-F 256 \\\ \n\t\t\t\t-@ $thread_str \\\ \n\t\t\t\t$merged_dedup_bam\\\ \n\t) \ \n\ \n$juicer_tools \\\ \n\tstatistics \\\ \n\t\t--threads $thread_str \\\ \n\t\t$site_file \\\ \n\t\t$stat_txt\\\ \n\t\t$merged_dedup_txt \\\ \n\t\t$genome_size_file \ \n\tcat \\\ \n\t\t${split_dir}/*.res.txt | \\\ \n\t$awk_cmd \\\ \n\t\t-v dups=\$dups \\\ \n\t\t-v ligation=$ligation \\\ \n\t\t-f ${common_dir}/stats_sub.awk \\\ \n\t> $stat_txt \ \n\t\ \n\t$juicer_tools \\\ \n\t\tstatistics \\\ \n\t\t\t--threads $thread_str \\\ \n\t\t\t$site_file \\\ \n\t\t\t$stat_txt\\\ \n\t\t\t$merged_dedup_txt \\\ \n\t\t\t$genome_size_file \ \n\ \nfi\ \n\ \n$juicer_tools \\\ \n\tpre \\\ \n\t\t-k KR,VC,SCALE \\\ Loading Loading
hic_generation.sh +25 −24 Original line number Diff line number Diff line Loading @@ -104,33 +104,34 @@ do \nexport _JAVA_OPTIONS=\"-Xmx60g -Xms60g\"\ \n\ \nif [ ! -e $stat_m ];then\ \ndups=\$(\\\ \n\t$samtools_cmd \\\ \n\t\tview \\\ \n\t\t\t-c \\\ \n\t\t\t-f 1089 \\\ \n\t\t\t-F 256 \\\ \n\t\t\t-@ $thread_str \\\ \n\t\t\t$merged_dedup_bam\\\ \n) \ \n\ \ncat \\\ \n\t${split_dir}/*.res.txt | \\\ \n$awk_cmd \\\ \n\t-v dups=\$dups \\\ \n\t-v ligation=$ligation \\\ \n\t-f ${common_dir}/stats_sub.awk \\\ \n> $stat_txt \ \n\tdups=\$(\\\ \n\t\t$samtools_cmd \\\ \n\t\t\tview \\\ \n\t\t\t\t-c \\\ \n\t\t\t\t-f 1089 \\\ \n\t\t\t\t-F 256 \\\ \n\t\t\t\t-@ $thread_str \\\ \n\t\t\t\t$merged_dedup_bam\\\ \n\t) \ \n\ \n$juicer_tools \\\ \n\tstatistics \\\ \n\t\t--threads $thread_str \\\ \n\t\t$site_file \\\ \n\t\t$stat_txt\\\ \n\t\t$merged_dedup_txt \\\ \n\t\t$genome_size_file \ \n\tcat \\\ \n\t\t${split_dir}/*.res.txt | \\\ \n\t$awk_cmd \\\ \n\t\t-v dups=\$dups \\\ \n\t\t-v ligation=$ligation \\\ \n\t\t-f ${common_dir}/stats_sub.awk \\\ \n\t> $stat_txt \ \n\t\ \n\t$juicer_tools \\\ \n\t\tstatistics \\\ \n\t\t\t--threads $thread_str \\\ \n\t\t\t$site_file \\\ \n\t\t\t$stat_txt\\\ \n\t\t\t$merged_dedup_txt \\\ \n\t\t\t$genome_size_file \ \n\ \nfi\ \n\ \n$juicer_tools \\\ \n\tpre \\\ \n\t\t-k KR,VC,SCALE \\\ Loading
