Loading README.md +4 −6 Original line number Diff line number Diff line Loading @@ -110,8 +110,8 @@ correction with up to 1 Hamming distance from a whitelist barcode. By setting Hamming distance from a whitelist barcode. User can also increase the probability threshold to make a correction by setting **--bc-probability-threshold** (set to 0.9 by default) to a large value (e.g., 0.975) to only make reliable corrections. Single-cell ATAC-seq data, such as 10x Genomics, may come in multiple lanes and have multiple read and barcode files, and you can use "," to add multiple files as [above](#general) corrections. For scATAC-seq data with multiple read and barcode files, you can use "," to concatenate multiple input files as the example [above](#general). #### <a name="map-hic"></a>Map Hi-C short reads Loading @@ -125,12 +125,10 @@ other than the one in the index. Therefore, Chromap provides the option **--chr- to specify the alignment order, and **--pairs-natural-chr-order** for flipping the pair in the pairs format. Detailed description of Chromap command line options and optional tags can be displayed by running "./chromap" or "./chromap -h". ### <a name="help"></a>Getting help If you encounter bugs or have further questions or requests, Detailed description of Chromap command line options and optional tags can be displayed by running Chromap with **-h**. If you encounter bugs or have further questions or requests, you can raise an issue at the [issue page][issue]. Loading Loading
README.md +4 −6 Original line number Diff line number Diff line Loading @@ -110,8 +110,8 @@ correction with up to 1 Hamming distance from a whitelist barcode. By setting Hamming distance from a whitelist barcode. User can also increase the probability threshold to make a correction by setting **--bc-probability-threshold** (set to 0.9 by default) to a large value (e.g., 0.975) to only make reliable corrections. Single-cell ATAC-seq data, such as 10x Genomics, may come in multiple lanes and have multiple read and barcode files, and you can use "," to add multiple files as [above](#general) corrections. For scATAC-seq data with multiple read and barcode files, you can use "," to concatenate multiple input files as the example [above](#general). #### <a name="map-hic"></a>Map Hi-C short reads Loading @@ -125,12 +125,10 @@ other than the one in the index. Therefore, Chromap provides the option **--chr- to specify the alignment order, and **--pairs-natural-chr-order** for flipping the pair in the pairs format. Detailed description of Chromap command line options and optional tags can be displayed by running "./chromap" or "./chromap -h". ### <a name="help"></a>Getting help If you encounter bugs or have further questions or requests, Detailed description of Chromap command line options and optional tags can be displayed by running Chromap with **-h**. If you encounter bugs or have further questions or requests, you can raise an issue at the [issue page][issue]. Loading
