Update README.md

### <a name="install"></a>Installation

You can acquire precompiled binaries from

the [release page][release] with:

```sh

curl -L https://github.com/haowenz/chromap/releases/download/v0.1/chromap-0.1_x64-linux.tar.bz2 | tar -jxvf -

./chromap-0.1_x64-linux/chromap

```

If you want to compile from the source, you need to have the GCC compiler, GNU make

To compile from the source, you need to have the GCC compiler, GNU make

and zlib development files installed. Then type `make` in the source code

directory to compile. 

```sh

chromap --preset chip -x index -r ref.fa -1 read1.fq.gz -2 read2.fq.gz -o aln.bed      # ChIP-seq reads

```

This set of parameters is tuned for mapping ChIP-seq reads. Chromap will trim the

adapters on 3' end, map the paired-end reads with max insert size (**-l**) up to

2000 and then remove duplicates.

This set of parameters is tuned for mapping ChIP-seq reads. Chromap will map the 

paired-end reads with max insert size up to 2000 (**-l 2000**) and then remove

duplicates (**--remove-pcr-duplicates**) using the low memory mode

(**--low-mem**). The output is in BED format (**--BED**). In the output BED file,

each row is a mapping of a fragment (i.e., a read pair) and the columns are

    chrom chrom_start chrom_end N mapq strand

The strand here is the strand of the first read in a read pair (specified by **-1**).

If the mapping start and end locations of each read in a read pair are desired,

**--TagAlign** should be used to overide **--BED** in the preset parameters as following

```sh

chromap --preset chip -x index -r ref.fa -1 read1.fq.gz -2 read2.fq.gz --TagAlign -o aln.tagAlign      # ChIP-seq reads

```

For each read pair, there will be two rows in the output file, one for each read in the pair

respectively. The meaning of the columns remains the same.

#### <a name="map-atac"></a>Map ATAC-seq/scATAC-seq short reads

chromap --preset atac -x index -r ref.fa -1 read1.fq.gz -2 read2.fq.gz -o aln.bed\

 -b barcode.fq.gz --barcode-whitelist whitelist.txt                                    # scATAC-seq reads

```

This set of parameters is tuned for mapping ATAC-seq/scATAC-seq reads.

Chromap will trim the adapters on 3' end (**--trim-adapters**), map the 

paired-end reads with max insert size up to 2000 (**-l 2000**) and then

remove duplicates at cell level (**--remove-pcr-duplicates-at-cell-level**).

Tn5 shift will also be applied to the fragments (**--Tn5-shift**). The 

forward mapping start positions are increased by 4bp and the reverse

mapping end positions are decreased by 5bp. The processing is run in

the low memory mode (**--low-mem**).

When barcodes and a whitelist are given as input, by default Chromap will

estimate barcode abundance and use this information to perform barcode

correction with up to 1 Hamming distance from a whitelist barcode. By setting

Chromap also supports user-defined barcode format, including mixed barcode and genomic 

data case. User can specify the sequence structure through option **--read-format**. The value

is comma-separated string, each field is also semi-comma-splitted string: [r1|r2|bc]:start:end.

The start and end(inclusive, -1 means to the read end). For the example that the barcode is in read1's 

first 16bp, one can use the option 

is a comma-separated string, each field in the string is also a semi-comma-splitted string

    [r1|r2|bc]:start:end

The start and end are inclusive and -1 means the end of the read. For example,

when the barcode is in the first 16bp of read1, one can use the option 

`-1 read1.fq.gz -2 read2.fq.gz --barcode read1.fq.gz --read-format bc:0:15,r1:16:-1`

The BED format (fragment file) for bulk and single-cell is different except for the first

The output file formats for bulk and single-cell data are different except for the first

three columns. For bulk data, the columns are

    chrom chrom_start chrom_end N mapq strand

```sh

chromap --preset hic -x index -r ref.fa -1 read1.fa -2 read2.fa -o aln.pairs           # Hi-C reads and pairs output

```

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]. 

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 

### <a name="help"></a>Getting help

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,

can be displayed by running Chromap with **-h** or by `man ./chromap.1`. If you encounter bugs or have further questions or requests,

you can raise an issue at the [issue page][issue].