sickle转录组数据过滤·使用案例

1. 安装sickle

conda install -c bioconda sickle
# failed

但是好像conda装的不能用，所以换个方法安装

wget  https://github.com/najoshi/sickle/archive/master.zip
unzip master.zip
cd sickle-master/
make
#在 .bashrc中 alias sickle='your path/sickel'
vi .bashrc

2. 运行sickle

sickle 的参数是这样的：

pe : use paired-end mode 
-f training/rnaseq/ERR022486_chr22_read1.fastq.gz : the fastq file for read 1 
-r training/rnaseq/ERR022486_chr22_read2.fastq.gz : the fastq file for read 2 
-t sanger : the quality encoding. All data downloaded from EBI or NCBI will be "sanger" encoded. For an explanation:<http://en.wikipedia.org/wiki/FASTQ_format#Encoding> 
-o ERR022486_chr22_read1_trim.fastq : the output file for trimmed reads from read 1 
-p ERR022486_chr22_read2_trim.fastq : the output file for trimmed reads from read 2 
-s ERR022486_chr22_single_trim.fastq : the output file for reads where the mate has failed the quality or length filter 
-q 30 : the quality value to use. Bases below this will be trimmed, using a sliding window 
-l 15 : the minimum length allowed after trimming. Here we remove reads with less than 15bp

运行代码：

~/installhere/sickle-master/sickle pe -f SRR11559267_1.fastq -r SRR11559267_2.fastq -t sanger -o trimmed_output_file1.fastq -p trimmed_output_file2.fastq -s other.fastq

展示结果

#展示结果
PE forward file: SRR11559267_1.fastq
PE reverse file: SRR11559267_2.fastq

Total input FastQ records: 222032 (111016 pairs)

FastQ paired records kept: 217534 (108767 pairs)
FastQ single records kept: 2248 (from PE1: 2237, from PE2: 11)
FastQ paired records discarded: 2 (1 pairs)
FastQ single records discarded: 2248 (from PE1: 11, from PE2: 2237)

$ls -tl
total 219128
-rw-rw-r-- 1 chenss chenss 52064560 Nov 25 21:19 trimmed_output_file2.fastq
-rw-rw-r-- 1 chenss chenss  1148435 Nov 25 21:19 other.fastq
-rw-rw-r-- 1 chenss chenss 54354638 Nov 25 21:19 trimmed_output_file1.fastq
-rw-rw-r-- 1 chenss chenss 57473850 Nov 24 19:25 SRR11559267_2.fastq
-rw-rw-r-- 1 chenss chenss 59332740 Nov 24 19:25 SRR11559267_1.fastq

为什么我的数据是illumina，此处是 -t sanger呢?
因为： After about 2012 (Illumina 1.8+) illumina uses sanger quality encoding