Jun Xu (junxu1048@genetics.ac.cn) 1,2 , Song Xu (sxu@genetics.ac.cn) 1,2, Fei Lu (flu@genetics.ac.cn) 1,3
1 State Key Laboratory of Plant Cell and Chromosome Engineering , Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences
2 University of Chinese Academy of Sciences
3 CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Simplified Poly(A) Anchored Sequencing (SiPAS) is a custom 3'RNA-seq method to boost population-level transcriptomic studies in plants. SiPAS simplifies current 3'RNA-seq approaches which are successful in quantifying gene expression in cultivated mammal cells. Also, it uses anchored oligo(dT) primers to obtain longer reads for accurate sequence alignment and gene expression quantification. SiPAS has three significant improvement:
1. On the premise of high accuracy, it minimizes the labor and cost for library construction.
2. It achieves high reproducibility -- only 5 million reads are needed to have a correlation coefficient of 0.94 between two replicates while being performed to quantify expresseon level of 12k genes in bread wheat.
3. SiPAS is universal. Given its success in hexaploid wheat, which has the largest and most complex genome of crops, we believe it can be used widely in many other plants.
At the same time, we launch the bioinformatic pipeline of SiPAS (SiPAS-Profiler), which performs gene expressino quantification through SIPAS data. Using raw RNA-seq data, gene expression table of a large population can be obtained immediately.
1. Parse samples2. Make index of reference3. Align to genome4. Quantitate gene expression5. Output count tableSTARHTSeqTo start your analysis, you need to provide some parameter files. There also some options you can choose.
SiPAS-Profiler
Author: Jun Xu, Fei Lu
Email: junxu1048@genetics.ac.cn; flu@genetics.ac.cn
Homepage: http://plantgeneticslab.weebly.com/
#This program is used for gene expression profiling from Simplified Poly(A) Anchored Sequencing (SiPAS)
#The usage is java -Xms10g -Xmx20g SiPAS-Profiler.jar parameters_SiPAS.txt > log.txt &
#Please keep the order of following parameters
#Mode of alignment. PE or SE. The default is PE mode
PE
#Number of loci of multiple alignment. If the value is 10, it means that a read mapping to more than 10 position will be discarded. The default is 2
2
#The rate of mismatch. If this value is greater than set value, this read will be discard. The defult is 0.1
0.1
#The minimun number of match
80
#The SampleInformation file (with header), the format is Taxa\tBarcode\tPlateName\tFastqPath
/Users/junxu/Documents/analysisL/softwareTest/sipas/input/SampleInformation.txt
#The directory of output
/Users/junxu/Documents/analysisL/softwareTest/sipas/output
#The gene annotation file (GTF format)
/Users/junxu/Documents/database/wheat/gene/v1.1/wheat_v1.1_Lulab.gtf
#The gene reference file (fa format)
/Users/junxu/Documents/database/wheat/reference/v1.0/ABD/abd_iwgscV1.fa
#The path of STAR alignment software
/Users/junxu/Software/STAR-2.5.4b/bin/MacOSX_x86_64/starTaxa Plate_ID Barcode FastqPath_R1 FastqPath_R2
PL-BC1 P1 TGAACACG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC2 P1 CGTTGTCA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC3 P1 TGAATCAG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC4 P1 TTCGACTG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC5 P1 CTTAGTTG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC6 P1 CGTGCTGA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC7 P1 CCTCAAGC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC8 P1 TGAGGACT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC9 P1 CGCGTTAT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC10 P1 CGTTTCAT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC11 P1 GCATAGTC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC12 P1 TGGCTCTA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC13 P1 CAAGGAAG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC14 P1 CAGTACCT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC15 P1 CGACTTGT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC16 P1 ATGCCTCA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC17 P1 TCTCAGAA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC18 P1 CTTCGTCT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC19 P1 TTCACATG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC20 P1 AAAGCGAG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC21 P1 CGCGAATC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC22 P1 TAGAGATC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC23 P1 CCCAAACA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC24 P1 TTGGAAAC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC25 P1 AGACTCGC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC26 P1 TTTTACCG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC27 P1 GCTAACGG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC28 P1 CATAACCC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC29 P1 TTCCCGCA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC30 P1 AACAGTTG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC31 P1 TAGCTAGC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC32 P1 GCAACTAG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC33 P1 GGTTTCGC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC34 P1 GAGTTACT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC35 P1 TCCAAGTC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC36 P1 TAGCATAC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC37 P1 ATCTAGGA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC38 P1 ATCATGTG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC39 P1 TCTCTAGT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC40 P1 AGGAAGAA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC41 P1 ACGACCTC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC42 P1 ACACGCCA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC43 P1 GTCAAGGT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC44 P1 CTCCCCTT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC45 P1 CGCAAAAT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC46 P1 GTTAGCGT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC47 P1 CCGGTGAA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC48 P1 ATTGTCCT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC49 P1 ACTGACTT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC50 P1 CGAGTAAA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC51 P1 TTACCGTG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC52 P1 CCAGATAC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC53 P1 GGTGATCT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC54 P1 TTTCTCCC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC55 P1 GACTCCCA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC56 P1 CTTTCCCT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC57 P1 CTACTGAC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC58 P1 GTGGGACT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC59 P1 CTAGCATC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC60 P1 TATCGGTC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC61 P1 TGCAGCTG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC62 P1 CAGGCGTA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC63 P1 TGCTTAAC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC64 P1 GTGTACAC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC65 P1 TTGCGGAT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC66 P1 TCATTGGA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC67 P1 GTACCCAC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC68 P1 GAATTGTG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC69 P1 CAGTTCGG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC70 P1 AGATGCTA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC71 P1 ATTGTGGC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC72 P1 ATGTAACC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC73 P1 CATGCCTT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC74 P1 CCTCTTAG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC75 P1 TACGAGCA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC76 P1 GGAAATTG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC77 P1 GCAAGACG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC78 P1 ACTTTGCG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC79 P1 GTGTGCTA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC80 P1 TGTTACGT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC81 P1 CTGAGACG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC82 P1 CCAGGCAA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC83 P1 GTCGCACA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC84 P1 GTCGACGA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC85 P1 GCCATTGG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC86 P1 GAGACCGA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC87 P1 GCGCCTTA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC88 P1 TTCAGTCC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC89 P1 CTTAGGCA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC90 P1 TCCTGTCA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC91 P1 AAGAGAGG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC92 P1 TCGTTAAG /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC93 P1 TGTCCCCA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC94 P1 CACATTCC /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC95 P1 CGGTGATA /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gz
PL-BC96 P1 ACGACTGT /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R1.fq.gz /Users/junxu/Documents/analysisL/softwareTest/sipas/input/sub1-1_R2.fq.gzjava -Xms10g -Xmx20g SiPAS-Profiler.jar parameters_SiPAS.txt > log.txt
When we construct libraries in HTS plate, the uneven output of libraries often occurs. In order to get the relatively consistent library output, the test data is usually used to assist. The result is as a reference to guide the large-scale sequencing. The testInfor.jar file is a new pipeline to parse the information in the data. The following are the statistical results.
From this file you can get the reads number, barcode of each sample (Rawdata) and the degree of uniformity between samples in library. This can be as the conduct for sample mixing within the library.
20190724S1-1 Barcode Reads number Ratio
A01 TGAACACG 809092 2.38%
A02 CGTTGTCA 742120 2.18%
A03 TGAATCAG 745732 2.19%
A04 TTCGACTG 288972 0.85%
A05 CTTAGTTG 461020 1.36%
A06 CGTGCTGA 393824 1.16%
A07 CCTCAAGC 77632 0.23%
A08 TGAGGACT 25560 0.08%
A09 CGCGTTAT 634040 1.86%
A10 CGTTTCAT 278692 0.82%
A11 GCATAGTC 241788 0.71%
A12 TGGCTCTA 140692 0.41%
B01 CAAGGAAG 188628 0.55%
B02 CAGTACCT 372328 1.09%
B03 CGACTTGT 840972 2.47%
B04 ATGCCTCA 379772 1.12%
B05 TCTCAGAA 324532 0.95%
B06 CTTCGTCT 388492 1.14%
B07 TTCACATG 68348 0.20%
B08 AAAGCGAG 36428 0.11%
B09 CGCGAATC 394444 1.16%
B10 TAGAGATC 423768 1.25%
B11 CCCAAACA 766728 2.25%
B12 TTGGAAAC 177076 0.52%Visually view the amount of data from the size of the file.
20190724S1-1 Reads number Base Mbase
A01 809092 242727600 81
A02 742120 222636000 65
A03 745732 223719600 65
A04 288972 86691600 26
A05 461020 138306000 41
A06 393824 118147200 35
A07 77632 23289600 8
A08 25560 7668000 4
A09 634040 190212000 55
A10 278692 83607600 25
A11 241788 72536400 22
A12 140692 42207600 13
B01 188628 56588400 18
B02 372328 111698400 33
B03 840972 252291600 81
B04 379772 113931600 34
B05 324532 97359600 29
B06 388492 116547600 35
B07 68348 20504400 7
B08 36428 10928400 5
B09 394444 118333200 35
B10 423768 127130400 38
B11 766728 230018400 81
B12 177076 53122800 17It can be used as an important basis for library mixing.
library clean data(Gbase) raw data(Gbase)
20190724S1-1 791483100 839794800
20190724S1-2 916298400 987440100
20190724S1-4 795152400 862199400
20190724S1-5 817035000 868636200
20190724S1-6 1659344400 1770141600
20190724S2-10 659848500 715755000
20190724S2-11 680722200 726794100
20190724S2-13 850248600 913733100 The use of pipeline is also very simple. For example:
java -jar testInfor.jar /Users/home/barcode.txt /Users/home/inputFileDirS
The first parameter "/Users/home/barcode.txt" is the path of barcode file which is used to parse samples and print this information in ratioTable.txt file. The second is the the path of the input directory. Under this directory, it must contain the folder of Rawdata and Cleandata which are both needed in the following analysis.
The generated files will not be used for subsequent analysis. So all intermediate files will be deleted at the end, leaving only the final result file.