转录组分析---Hisat2+StringTie+Ballgown使用

转录组分析---Hisat2+StringTie+Ballgown使用

  (2016-10-10 08:14:45)

转载▼

标签：  生物信息学   转录组

1.Hisat2建立基因组索引：

First, using the python scripts included in the HISAT2 package, extract splice-site and exon information from the gene

annotation file:

 

$ extract_splice_sites.py gemome.gtf >genome.ss#得到剪接位点信息

$ extract_exons.py genome.gtf >genome.exon#得到外显子信息

 

Second, build a HISAT2 index:

 

$ hisat2-build --ss genome.ss --exon genome.exon genome.fa genome

 

备注extract_splice_sites.py 和 extract_exons.py 在hisat2软件包中涵盖了，这两步不是必须的，只是为了发现剪切位点，也可以直接：

$ hisat2-build   genome.fa genome

 

2. 利用hisat2比对到基因组：

 

hisat2 -p 8 --dta -x genome -1 file1_1.fastq.gz -2 file1_2.fastq.gz -S file1.sam

hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran -1 file2_1.fastq.gz -2 file2_2.fastq.gz -S file2.sam

 

备注：--dta:输出转录组型的报告文件

-x：基因组索引

-S : 输出sam文件

-p: 线程数

其他参数：

Input:

  -q                 query input files are FASTQ .fq/.fastq (default)

  --qseq             query input files are in Illumina's qseq format

  -f                 query input files are (multi-)FASTA .fa/.mfa

  -r                 query input files are raw one-sequence-per-line

  -c                 , , are sequences themselves, not files

  -s/--skip    skip the first reads/pairs in the input (none)

  -u/--upto    stop after first reads/pairs (no limit)

  -5/--trim5   trim bases from 5'/left end of reads (0)

  -3/--trim3   trim bases from 3'/right end of reads (0)

  --phred33          qualities are Phred+33 (default)

  --phred64          qualities are Phred+64

  --int-quals        qualities encoded as space-delimited integers

 

 Alignment:

  -N           max # mismatches in seed alignment; can be 0 or 1 (0)

  -L           length of seed substrings; must be >3, <32 (22)

  -i          interval between seed substrings w/r/t read len (S