fix small typo in README (73cc0f35) · Commits · github_fork / Chromap

README.md

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		@@ -25,7 +25,7 @@ cd chromap && make
		- [Map ChIP-seq short reads](#map-chip)
		- [Map ATAC-seq/scATAC-seq short reads](#map-atac)
		- [Map Hi-C short reads](#map-hic)
		- [Summarizing mapping statistcs/quality control](#atacseq-qc)
		- [Summarizing mapping statistics/quality control](#atacseq-qc)
		- [Summary File](#summaryfile)
		- [Estimating FRiP](#estfrip)
		- [Features to assist in doublet detection](#doublet)
		@@ -128,7 +128,7 @@ chromap --preset hic -x index -r ref.fa -1 read1.fa -2 read2.fa -o aln.pairs
		```
		Chromap will perform split alignment (--split-alignment) on Hi-C reads and output mappings in [pairs][pairs] format (--pairs), which is used in [4DN Hi-C data processing pipeline][4DN]. 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 alignment order, and --pairs-natural-chr-order for flipping the pair in the pairs format.

		### <a name="atacseq-qc"></a>Summarizing mapping statistcs/quality control
		### <a name="atacseq-qc"></a>Summarizing mapping statistics/quality control

		Chromap allows you to summarize the dataset's mapping statistics as well as quality metrics at either a bulk or single cell level. To enable this feature, users can specify a file path using this option, --summary [FILE], where a csv file will be saved.