Skip to content
BranchesTags

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

569 Commits
4CfastqAnalysis.sh
4CfastqAnalysis.sh
 
 
4CfastqProcessing.sh
4CfastqProcessing.sh
 
 
AllAdaptors.fa
AllAdaptors.fa
 
 
BelindaParaScan.sh
BelindaParaScan.sh
 
 
BowtieCodeGenerator.sh
BowtieCodeGenerator.sh
 
 
BowtieCodeGeneratorYichengTotalRNArRNARemoval.sh
BowtieCodeGeneratorYichengTotalRNArRNARemoval.sh
 
 
BowtieYichengCodeGenerator.sh
BowtieYichengCodeGenerator.sh
 
 
BowtieYichengCodeGeneratorChIP.sh
BowtieYichengCodeGeneratorChIP.sh
 
 
BowtieYichengCodeGeneratorRNA.sh
BowtieYichengCodeGeneratorRNA.sh
 
 
BowtieYichengCodeGeneratorsmallRNA.sh
BowtieYichengCodeGeneratorsmallRNA.sh
 
 
BowtieYichengCodeGeneratorsmallRNA181109.sh
BowtieYichengCodeGeneratorsmallRNA181109.sh
 
 
BowtieYichengCodeGeneratorsmallRNA190118.sh
BowtieYichengCodeGeneratorsmallRNA190118.sh
 
 
BowtieYichengCodeGeneratorsmallRNA191016.sh
BowtieYichengCodeGeneratorsmallRNA191016.sh
 
 
BowtieYichengCodeGeneratorsmallRNA191026TE.sh
BowtieYichengCodeGeneratorsmallRNA191026TE.sh
 
 
BowtieYichengCodeGeneratorsmallRNA220421.sh
BowtieYichengCodeGeneratorsmallRNA220421.sh
 
 
BowtieYichengCodeGeneratorsmallRNA220424TE.sh
BowtieYichengCodeGeneratorsmallRNA220424TE.sh
 
 
ChIP-seq.md
ChIP-seq.md
 
 
Cleanup.sh
Cleanup.sh
 
 
CodeChange.sh
CodeChange.sh
 
 
CoverageBigWig.sh
CoverageBigWig.sh
 
 
CufflinksCode.sh
CufflinksCode.sh
 
 
DEseqRun.sh
DEseqRun.sh
 
 
DatabaseGenerator.sh
DatabaseGenerator.sh
 
 
DownloadFolder.sh
DownloadFolder.sh
 
 
ENCODEDownloader.sh
ENCODEDownloader.sh
 
 
ENCODESampleListGenerator.sh
ENCODESampleListGenerator.sh
 
 
ENCODESampleListGenerator2.sh
ENCODESampleListGenerator2.sh
 
 
FastQCTrim.sh
FastQCTrim.sh
 
 
FastQCTrimDeep.sh
FastQCTrimDeep.sh
 
 
FastQCTrimShuaiWangRibo.sh
FastQCTrimShuaiWangRibo.sh
 
 
FastQCTrimYicheng.sh
FastQCTrimYicheng.sh
 
 
FseqCode.sh
FseqCode.sh
 
 
GECjumpgateCodeGenerator4C.sh
GECjumpgateCodeGenerator4C.sh
 
 
GECjumpgateCodeGeneratorATAC.sh
GECjumpgateCodeGeneratorATAC.sh
 
 
GECjumpgateCodeGeneratorRNAseq.sh
GECjumpgateCodeGeneratorRNAseq.sh
 
 
GECjumpgateCodeGeneratorShuaiWangRibo.sh
GECjumpgateCodeGeneratorShuaiWangRibo.sh
 
 
GECjumpgateCodeGeneratorYichengChIP.sh
GECjumpgateCodeGeneratorYichengChIP.sh
 
 
GECjumpgateCodeGeneratorYichengRNAseq.sh
GECjumpgateCodeGeneratorYichengRNAseq.sh
 
 
GECjumpgateCodeGeneratorYichengpiRNA.sh
GECjumpgateCodeGeneratorYichengpiRNA.sh
 
 
GECjumpgatePasswords.sh
GECjumpgatePasswords.sh
 
 
GECrefolder.sh
GECrefolder.sh
 
 
GECrefolderShuaiWangRibo.sh
GECrefolderShuaiWangRibo.sh
 
 
GEOCodeGeneratorATAC.sh
GEOCodeGeneratorATAC.sh
 
 
GEOCodeGeneratorRNAseq.sh
GEOCodeGeneratorRNAseq.sh
 
 
GEOSampleListGenerator.sh
GEOSampleListGenerator.sh
 
 
GEOrefolder.sh
GEOrefolder.sh
 
 
GenomeDefinitions.sh
GenomeDefinitions.sh
 
 
HOMERCode.sh
HOMERCode.sh
 
 
HTseqCodeGenerator.sh
HTseqCodeGenerator.sh
 
 
LocalCodeGeneratorATAC.sh
LocalCodeGeneratorATAC.sh
 
 
LocalCodeGeneratorCLIPseq.sh
LocalCodeGeneratorCLIPseq.sh
 
 
LocalCodeGeneratorRNAseq.sh
LocalCodeGeneratorRNAseq.sh
 
 
LocalCodeGeneratorYichengCLIP.sh
LocalCodeGeneratorYichengCLIP.sh
 
 
LocalCodeGeneratorYichengChIP.sh
LocalCodeGeneratorYichengChIP.sh
 
 
LocalCodeGeneratorYichengRNAseq.sh
LocalCodeGeneratorYichengRNAseq.sh
 
 
LocalCodeGeneratorYichengTotalRNAseq.sh
LocalCodeGeneratorYichengTotalRNAseq.sh
 
 
LocalCodeGeneratorYichengpiRNA.sh
LocalCodeGeneratorYichengpiRNA.sh
 
 
LocalCodeGeneratorYichengpiRNA19_30.sh
LocalCodeGeneratorYichengpiRNA19_30.sh
 
 
LocalCodeGeneratorYichengpiRNA210822.sh
LocalCodeGeneratorYichengpiRNA210822.sh
 
 
Localrefolder.sh
Localrefolder.sh
 
 
LocalrefolderCLIP.sh
LocalrefolderCLIP.sh
 
 
MitoBlackRun.sh
MitoBlackRun.sh
 
 
NovelCharacterDefinition.sh
NovelCharacterDefinition.sh
 
 
QuickBowtie.sh
QuickBowtie.sh
 
 
README.md
README.md
 
 
RNAseQC.sh
RNAseQC.sh
 
 
RsemCodeGenerator.sh
RsemCodeGenerator.sh
 
 
STARCodeGenerator.sh
STARCodeGenerator.sh
 
 
STARCodeGeneratorYicheng.sh
STARCodeGeneratorYicheng.sh
 
 
STARbigWigCoverageCode.sh
STARbigWigCoverageCode.sh
 
 
STARbigWigCoverageCodeYicheng.sh
STARbigWigCoverageCodeYicheng.sh
 
 
SampleListGenerator.sh
SampleListGenerator.sh
 
 
SamtoolsSort.sh
SamtoolsSort.sh
 
 
SamtoolsSortBulk.sh
SamtoolsSortBulk.sh
 
 
SpeciesReporter.sh
SpeciesReporter.sh
 
 
SppQC.sh
SppQC.sh
 
 
Stats.sh
Stats.sh
 
 
TophatCLIPCodeGenerator.sh
TophatCLIPCodeGenerator.sh
 
 
TophatCodeGenerator.sh
TophatCodeGenerator.sh
 
 
TophatCufflinksStats.sh
TophatCufflinksStats.sh
 
 
TophatbigWigCode.sh
TophatbigWigCode.sh
 
 
TrackSummary.sh
TrackSummary.sh
 
 
bigWigCode.sh
bigWigCode.sh
 
 
bigWigCodePython2on3.sh
bigWigCodePython2on3.sh
 
 
deseq2.Rscript
deseq2.Rscript
 
 
eRangeCode.sh
eRangeCode.sh
 
 
hotspot2Code.sh
hotspot2Code.sh
 
 
piRNA_PostProcess_19_30.sh
piRNA_PostProcess_19_30.sh
 
 
piRNA_PostProcess_23_29.sh
piRNA_PostProcess_23_29.sh
 
 
piRNA_PostProcess_50.sh
piRNA_PostProcess_50.sh
 
 
piRNA_PostProcess_Before20220423.sh
piRNA_PostProcess_Before20220423.sh
 
 
piRNA_PostProcess_TE.sh
piRNA_PostProcess_TE.sh
 
 
piRNA_U_bias.sh
piRNA_U_bias.sh
 
 
signature.py
signature.py
 
 
smallRNA-seq.md
smallRNA-seq.md
 
 
totalRNA-seq__OR__RIP.md
totalRNA-seq__OR__RIP.md
 
 

Repository files navigation

⚠️⚠️Repo MOVED to HERE ⚠️⚠️!

⚠️⚠️Updated Folder HERE⚠️⚠️!

⚠️⚠️Newer version HERE ⚠️⚠️!

Code generator instructions

  • This is a set of scripts to generate command-line scripts to handle sequencing data (the codes to write codes)
  • It generates codes to download data from Igor's website and codes for sequencing analysis

smallRNA-seq

  • downloading, trimming, genome mapping, vector mapping, bin calculation, ping-pong analyses etc.
  • more information about the generated code can be found here

totalRNA-seq/RIP-seq

  • downloading, trimming, rRNA removal, transcriptome mapping, vector mapping, bin calculation, phasing etc.

polyA-RNA-seq

  • downloading, trimming, transcriptome mapping, FPKM/TPM calculation, track generation etc.

ATAC-seq

  • downloading, trimming, genome mapping, normalization, peak calling, track generation etc.

4C-seq

ChIP-seq

About

No description, website, or topics provided.

Resources

Readme
Activity

Stars

0 stars

Watchers

1 watching

Forks

0 forks
Report repository

Releases

Packages

Contributors

Languages