Assembly of the Venom Gland Transcriptome from Tiger Snake
Data in this repository is structured using the following layout:
| Root | Files | Description |
|---|---|---|
0_rawData |
FastQC/*fastqc.html |
Individual Fastqc summaries |
FastQC/*fastqc.zip |
Data for each Fastqc report | |
FastQC/ngsReports_Fastqc.Rmd/.html |
ngsReport of Fastqc summaries for raw data | |
seqkitstatsRAW.tsv |
Tab delimited file containing seqkit statistics | |
1_trimmedData |
FastQC/*fastqc.html |
Individual Fastqc summaries |
FastQC/ngsReports_Fastqc.Rmd/.html |
ngsReports of Fastqc summaries for trimmed data | |
seqkitstatsTRIM.tsv |
Tab delimited file containing seqkit statistics | |
scripts |
adapterRemoval.sh |
shell script for removal of adapters and low quality scoring bases |
fastqc.sh |
shell script for fastqc reports of raw data | |
mergereads.sh |
shell script to merge raw reads together | |
trimmedfastqc.sh |
shell script for fastqc reports of trimmed data | |
seqkitstatsRAW.sh |
shell script for applying seqkit statistic function to raw data | |
seqkitstatsTRIM.sh |
shell script for applying seqkit statistic function to trimmed data | |
trinityInitial.sh |
shell script to run the Trinity De novo assmembler on trimmed data | |
soapDeNovoTransInitial.sh |
shell script to run the Soap De novo-Trans assembler on trimmed data | |
bowtie2SoapDeNovoInitial.sh |
shell script to assess read alignment of reads to Soap De novo-Trans transcriptome assembly | |
bowtie2TrinityInitial.sh |
shell script to assess read alignment of reads to Trinity De novo transcriptome assembly | |
fullLengthTranscriptsTrinityInitial.sh |
shell script to assess full length transcripts which match to known proteins | |
basicStatsTrinDN.sh |
shell script to assess basic contig and assembly statistics | |
transRateTrinity.sh |
shell script to run the transRate assembly quality assessment | |
TrinDN_BUSCO_metazoa.sh |
shell script alignment of transcriptome to the metazoan BUSCO gene set | |
TrinDN_BUSCO_tetrapoda.sh |
shell script alignment of transcriptome to the tetrapoda BUSCO gene set | |
TrinDN_BUSCO_vertebrata.sh |
shell script alignment of transcriptome to the vertebrata BUSCO gene set | |
CDHIT_TrinityDN.sh |
shell script running CDHIT program on Trinity De novo transcriptome assembly to cluster similar proteins | |
cdHIT_readRep.sh |
shell script to assess read alignment of reads to Trinity De novo transcriptome after removing redundancy | |
cdHIT_basicStats.sh |
shell script assessing basic statistics of Trinity De novo transcriptome after removing redundancy | |
cdHIT_fullCodingGenesBLAST.sh |
shell script assessing full length transcripts which match to known proteins in the Trinity De novo transcriptome after removing redundancy | |
cdHIT_busco_metazoa.sh |
shell script assessing alignment of the transcriptome produced by CD-HIT to the metazoa BUSCO gene set | |
cdHIT_busco_tetrapoda.sh |
shell script assessing alignment of the transcriptome produced by CD-HIT to the tetrapoda BUSCO gene set | |
cdHIT_busco_vertabrata.sh |
shell script assessing alignment of the transcriptome produced by CD-HIT to the vertebrata BUSCO gene set | |
cdHIT_ExN50.sh |
shell script to produce E90N50 statistic | |
cdHIT_transRate.sh |
shell script to run the transRate assembly quality assessment on the Trinity De novo transcriptome after removing redundancy | |
cdHIT_kallistoIndex.sh |
shell script to produce the Kallisto Index in order to run the Kallisto expression quantification step | |
cdHIT_kallistoQuant.sh |
shell script to run Kallisto quantification step | |
cdHIT_expressionMatrices.sh |
shell script produce matrices of raw expression counts, TPM normalised expression values and TMM normalised expression values | |
cdHIT_expressionCounts.sh |
shell script to produce counts of normalised TPM expression matrices | |
RawDataSummary.Rmd/.html |
source code and html file for summary of raw and trimmed data | |
AssemblyComparison.Rmd/.html |
source code and html file of assembly comparison statistics | |
BUSCOs.Rmd/.html |
source code and html file for the BUSCOs comparison for Trinity De novo assembly before and after reducing redundancy | |
CDHITTranscriptAndGeneQuant.Rmd/.html |
source code and html file for the downstream analysis for the Trinity De novo assembly before and after reducing redundancy | |
TranscriptQuant.Rmd/.html |
source code and html file for the downstream analysis of the Trinity De novo assembly before using CDHIT to reduce redundancy |