SuperTranscript specifications

Information


Unique identifier OMICS_12974
Name SuperTranscript
Alternative name Lace
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Group of transcripts, de novo contigs, reference sequence, long reads (or a mixture of all the above)
Input format FASTA, TXT
Output format FASTA, GFF, PSL, PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
Computer skills Advanced
Stability Stable
Requirements
Pandas, Networkx, Numpy, Matplotlib
Maintained Yes

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Documentation


Maintainer


  • person_outline Alicia Oshlack <>

Additional information


https://github.com/Oshlack/Lace

Publication for SuperTranscript

SuperTranscript in publications

 (6)
PMCID: 5240446
PMID: 28093077
DOI: 10.1186/s13059-016-1135-5

[…] a method for efficiently detecting de novo mutation using k-mer counting instead of reference-guided alignment. alicia oshlack (murdoch childrens research institute, australia) presented the supertranscript model for enhancing transcriptome visualization (https://github.com/oshlack/lace/wiki). jouni sirén (wellcome trust sanger institute, uk) presented a method to index population […]

PMCID: 3670878
PMID: 23755133
DOI: 10.1371/journal.pone.0064643

[…] differences between treatments . for qrt-pcr analysis, total rna from three biological replicates was isolated (qiagen, germany) from shoots of he and nhe, and reverse transcribed using the supertranscript iii rt kit (invitrogen, usa) according to the manufacturer’s instructions. for primer design (), blast searches were conducted against the arabidopsis nucleotide database with s. […]

PMCID: 3276278
PMID: 21979946
DOI: 10.1093/hmg/ddr459

[…] the manufacturer's protocol, and subsequently treated with dnase i (invitrogen, carlsbad, ca, usa). dnase-treated total rna from each lcl was reverse-transcribed into cdna using random primers and supertranscript™ iii reverse transcriptase (invitrogen), as specified by the manufacturer. pcr was performed using sybr green pcr master mix and run on 7500 real time pcr machine (applied biosystem, […]

PMCID: 3125268
PMID: 21663663
DOI: 10.1186/1471-2164-12-305

[…] included data on transcript isoforms was removed from the refseq table by allowing gene symbols only once within the refseq table. transcripts sharing a gene symbol were artificially fused to a 'supertranscript', so that expression of either isoform led to detection of the corresponding gene symbol. reads were randomly drawn and removed from the entirety of matched reads. drawn reads located […]

PMCID: 3000677
PMID: 20926450
DOI: 10.1093/hmg/ddq434

[…] valencia, ca, usa) according to the manufacturer's protocol, and subsequently treated with dnase i (invitrogen). dnase-treated total rna was reverse-transcribed into cdna using random primers and supertranscript™ iii reverse transcriptase (invitrogen), as specified by the manufacturer. polymerase chain reaction was performed using sybr green pcr master mix and run on 7500 real time pcr […]


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SuperTranscript institution(s)
Murdoch Childrens Research Institute, Royal Children’s Hospital, Victoria, Australia; School of BioSciences, University of Melbourne, Victoria, Australia
SuperTranscript funding source(s)
This project was funded by an NHMRC Career Development Fellowship APP1051481.

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