User:Konrad U Foerstner/Tools and procedures

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Contents

NGS

  • sambamba - offers similar functions as samtools but offers parallel processing

SNP calling

With Samtools

Phylogenetic trees

Multiple alignments

TSS prediction

Whole genome alignments

Pathway visualization

Transcription Terminator prediction

miRNA target prediction

miRmap (untested)

Differential gene expression analysis

DESeq

  • Tips:
    • small count noise - sequence deeper
    • large count noise - sequence more replicates
    • if the assumption that most genes are not differentially expressed is not the case use different methods to normalize (e.g. spike-ins)

Others

  • BaySEq
  • edgR
  • Gfold
  • NoiSeq

Python

General useful libraries

Misc


Visualisation

Personal tools