Package: stringtie (2.2.1+ds-3)

[ Source: stringtie  ]

assemble short RNAseq reads to transcripts

The abundance of transcripts in a human tissue sample can be determined by RNA sequencing. The exact sequence sampled may be random, depending on the technology used. And it may be short, i.e. shorter than the transcript. At some point, many shorter reads need to be assembled to the model the complete transcripts.

StringTie knows how to assemble of RNA-Seq into potential transcripts without the need of a reference genome and provides a quantification also of the splice variants.

Other Packages Related to stringtie

• dep: libc6 (>= 2.34)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libgcc-s1 (>= 3.4) [amd64, i386, mips64el]

  GCC support library

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

• dep: libhts3 (>= 1.17)

  C library for high-throughput sequencing data formats

• dep: libstdc++6 (>= 4.1.1)

  GNU Standard C++ Library v3

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• rec: stringtie-examples

  Package not available

• sug: cufflinks

  Transcript assembly, differential expression and regulation for RNA-Seq

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armel	342.3 kB	971.0 kB	[list of files]
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