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-->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).
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 |
Reference | Description |
---|---|
GENCODE_HG38 | GENCODE reference gene annotation for human genome hg38 |
HISAT2_HG38 | hisat2 index for hg38 |