DAtools is a command tool kit for gathering common data analysis scripts using java language, which was mainly developed and run myself. This project provided series of analysis function as well as pipeline applying for daily data analysis tasks.
##Screen shoot of DAtools
##Function gallary
0. BED Process :
java -jar DAtools.jar -bed
1. Devided fastq into two file by length :
java -jar DAtools.jar -devidedFastQbylength length all.fq out1.fq out2.fq
2. Dose ComposationFunctions :
java -jar DAtools.jar -dose
3. Draw genelength Distribution :
java -jar DAtools.jar -genelengthDis
4. Exome-seq function
java -jar DAtools.jar -exome
5. Extract expression data from cufflinks outputfile :
java -jar DAtools.jar -getcufflinksExpress cuffout_dir
6. Extract fastaSequence by idfile :
java -jar DAtools.jar -extractFastabyID fastafile idfile(one id in one line) outfile)
7. Functions to convert file format :
java -jar DAtools.jar -convertFormat
8. Generate a Ven plot by certain data input:
java -jar DAtools.jar -venplot datafile maintext plotType
9. Getovelap of two list with unique output:
java -jar DAtools.jar -getoverlap filelist1 filelist2 outputfile uniqueA uniqueB
10. Getovelap of two list:
java -jar DAtools.jar -getoverlap filelist1 filelist2 outputfile
11. Kegg Analysis :
java -jar DAtools.jar -kegg
12. Local GO mapping of gene list :
java -jar DAtools.jar -gomap obofile annotation nametype(1 for uniprotID(new);2 for geneSympol) genelistfile output
13. MetaGenome analysis :
java -jar DAtools.jar -meta
14. Multi mapfile merged to matrix
java -jar DAtools.jar -multi2matrix dir suffix outputfile
15. Procesing FastQ files :
java -jar DAtools.jar -fastqP
16. Process Fasta files
java -jar DAtools.jar -Fasta
17. Processing Excel format :
java -jar DAtools.jar -excel
18. RNAseq Differential Expression Analysis(M):
java -jar DAtools.jar -RNAseqDE -mode WR(orSC) condition1 condition2 outputfile
19. RNAseq Mappng/quantitifaction(M):
java -jar DAtools.jar -RNAseqpipe <fastq1> <fastq2> <library> <gtf>
20. Remove SUMO-FC adaptors :
java -jar DAtools.jar -removeAdapter fastafile adapter(TATA,CACA,GAGA) type(N/C)
21. Seperate fastq File by index :
java -jar DAtools.jar -sepFastq fastaqfile indexmapfile
22. SepfastaFilebyIndex :
java -jar DAtools.jar -sepFastabyIndex fastafile indexlist(TATA,CACA,GAGA)
23. Shorter sequencename of genome seq to parse gtg files :
java -jar DAtools.jar -genomenamecut genome.fa out.fa
24. Split the xml file generated by blast :
java -jar DAtools.jar -BlastXMLsplit fileinputxml seqnumber
25. Summary the unigenes distribution with trinity's output(Decreased) :
java -jar DAtools.jar -unigenedistribution isunigene trinity.fasta
##Designers:
Qi Zhao, zhaoqi3@mail2.sysu.edu.cn
Qi Zhao, zhaoqi3@mail2.sysu.edu.cn
Qi Zhao
Please feel free contact us.
Not implemented yet