Statistical Analysis Software Portable
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Six samples were sequenced on the Illumina HiSeq 2000, and the raw data were converted into the FASTQ files. The raw data were trimmed by Trimmomatic (). The Trimmomatic software was used to remove the low-quality bases and adaptor sequences. Trimmed reads were aligned to the human genome reference sequence (GRCh37) and mapped to the human reference genome by the BWA software (, version 0.6.1) to generate the BAM files. The BAM files were sorted by the SAMtools software (, version 0.1.19), and then the reads were generated in the BED format by the BEDtools software (, version 2.19.1). Reads were converted into the BAM format by the BEDtools software.
The raw libraries were sequenced on the Illumina HiSeq 2000 platform. After the base calling of the raw data, we used the Cutadapt program (, version 1.3.1) to remove the low-quality base pairs and adaptor sequences from the raw data. We aligned the clean data to the human genome reference sequence (GRCh37) and used the BWA software (, version 0.6.1) to map the clean data to the human reference genome. The SAMtools software (, version 0.1.19) was used to remove the multiple mapping reads and sort the SAM files. Processed data were converted to BAM files using SAMtools. Reads were generated in the BED format, and BEDtools (, version 2.19.1) was used to convert the BED files into a feature file. The BEDtools software was used for the alignment of the feature files and counting the reads to generate the value files.
SeqCode is a free, open-source software that performs statistical analysis and graphical analyses of aligned BAM files. SeqCode's graphical analysis and data mining tools are based on the JBrowse genome browser technology, which is capable of displaying and analyzing large-scale genomic sequencing data (such as whole-genome sequencing and ChIP-seq), which can be obtained either from a desktop or a web server. The bioinformatic software is written in ANSI C and is highly portable, cross-platform compatible and can be easily deployed on any type of Linux, Windows or MacOS operating system. 827ec27edc