cutNapAdapter

cutNapAdapter: A computational software for cutting adapters of non-capped RNA from NAP-seq data.

Overview:

cutNapAdapter is a software to cut both specific adapters and random barcodes of non-capped RNA from NAP-seq data.

Usage:

Usage: cutNapAdapter [options] -a -b -1 <read1 fiile, gzip format> -2 <read2 File, gzip format>
[options]
-o/--output : output dir[default=cutNapAdapterResults]
-f/--prefix : prefix for output files[default=cutNapAdapter]
-a/--adapter1 : adapter1 sequence [required]
-b/--adapter2 : adapter2 sequence [required for paired-end sequencing]
-c : barcode length of 5'-end[default=6]
-C : barcode length of 3'-end[default=6]
-m/--min-match : minimum matches bewteen adapter and sequences[default=5]
-l/--min-len : minimum sequence length after trim adapter[default=5]
-e/--error-rate : maximum error rate [default<=0.1]
-v/--verbose : verbose information
-V/--version : cutNapAdapter version
-h/--help : help informations

Installation:

Typical install time: within 5 min.
Download cutNapAdapter-1.0.tar.gz from https://github.com/junhong-huang/cutNapAdapter/releases ; unpack it, and make:
tar -xzvf cutNapAdapter-1.0.tar.gz
cd cutNapAdapter-1.0
make

System requirements:

Operating system: cutNapAdapter is designed to run on POSIX-compatible platforms, including UNIX, Linux and Mac OS/X. We have tested most extensively on Linux and MacOS/X because these are the machines we develop on.
Compiler: The source code is compiled with the C++ compiler g++. We test the code using the g++ compilers.
By default, cutNapAdapter does not require any additional libraries to be installed by you.

run cutNapAdapter:

cutNapAdapter -l 15 -e 0.1 -c 6 -o $outdir -f $prefix -a $adapter1 -b $adapter2 -1 $read1File -2 $read2File

Output:

The file format of ouput is the same as the input (fq.gz), which can be a direct input as the read mapper STAR or other mappers

Contact :

*****************************************************************************************
* cutNapAdapter - A computational software for cutting adapters of non-capped RNA from NAP-seq data.
*
* Author : Jian-Hua Yang yangjh7@mail.sysu.edu.cn
*
* RNA Information Center, School of Life Sciences, Sun Yat-Sen University
*
* Create date: 02/07/2022
*
* last modified time: 02/07/2022
****************************************************************************************