Loading README.md +2 −2 Original line number Diff line number Diff line Loading @@ -119,9 +119,9 @@ chromap --preset hic -x index -r ref.fa -1 read1.fa -2 read2.fa -o aln.pairs ``` Chromap will perform split alignment on Hi-C reads and output mappings in [pairs][pairs] format, which is used in [4DN Hi-C data processing pipeline][4DN]. Certain Hi-C data analysis pipeline requires the reads are sorted in specific order Some Hi-C data analysis pipelines may require the reads are sorted in specific chromosome order other than the one in the index. Therefore, Chromap provides the option **--chr-order** to specify the sort order, and **--pairs-natural-chr-order** for flipping the pair to specify the alignment order, and **--pairs-natural-chr-order** for flipping the pair in the pairs format. Loading Loading
README.md +2 −2 Original line number Diff line number Diff line Loading @@ -119,9 +119,9 @@ chromap --preset hic -x index -r ref.fa -1 read1.fa -2 read2.fa -o aln.pairs ``` Chromap will perform split alignment on Hi-C reads and output mappings in [pairs][pairs] format, which is used in [4DN Hi-C data processing pipeline][4DN]. Certain Hi-C data analysis pipeline requires the reads are sorted in specific order Some Hi-C data analysis pipelines may require the reads are sorted in specific chromosome order other than the one in the index. Therefore, Chromap provides the option **--chr-order** to specify the sort order, and **--pairs-natural-chr-order** for flipping the pair to specify the alignment order, and **--pairs-natural-chr-order** for flipping the pair in the pairs format. Loading
