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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie

ID: 01269439-28F0-F1BD-3B4A-38604657DBD3

This protocol is derived from a paper published on the journal Nature Protocols (Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown).

Environment

  • Operation System: Linux/Unix
  • CPU cores: 16
  • Memory: 64GB

Steps

Software Parameter
hisat2 -p {{ThreadN}} --dta -x {{HISAT2_HG38}} -1 {{InputFile:1}} -2 {{InputFile:2}} -S {{JobName}}.sam
samtools sort -@ {{ThreadN}} -o {{JobName}}.sorted.bam {{JobName}}.sam
stringtie -p {{ThreadN}} -G {{GENCODE_HG38}} -o {{JobName}}.gtf -l {{JobName}} {{JobName}}.sorted.bam

References

Reference Description
GENCODE_HG38 GENCODE reference gene annotation for human genome hg38
HISAT2_HG38 hisat2 index for hg38
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