How to use StringTie

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Instructions for using StringTie:

Stringtie [- G] [- l] [- o] [- p]

[- v] [- a] [- m] [- j] [- f]

[- C] [- c] [- g] [- u]

[- e] [- x] [- A] [- h] {- B |-b}

Options:

-- version: outputs the version information of the software

Gene annotation file of-G reference sequence (GTF/GFF3)

-l output the name prefix of the transcript (default: STRG)

-f the proportion of minimum transcripts (default: 0.1)

-minimum length of the assembled transcript (default: 200)

-o assemble the GTF comment file of the transcript (default: stdout)

-a minimum length of the anchoring sequence of the link site (default: 10)

Minimum coverage of the-j junction site (default: 1)

-t revise the predicted transcript based on coverage (default: coverage trimming is enabled)

-C minimum reads coverage of assembled transcripts (default: 2.5)

-v output log information

If the reads spacing on the-g comparison is greater than the threshold, a new transcriptional beam in Metro (default: 50)

-C output the transcript covered by reads in the reference transcript

-M transcription beam allows for the maximum proportion of reads coverage (default:0.95)

-number of threads (CPU) (default: 1)

-A gene Fengdu output file

-B outputs the Ballgown table file in the same directory as the exported GFT

-b output Ballgown table files in the directory

-e Fengdu evaluation of reference transcripts only (requires-G)

-x does not assemble any new transcripts in the reference sequence area

-u Multi-comparison correction (default: correction enabled)

-h output help information for the software

Instructions for the use of transcript merge mode:

Stringtie-- merge [Options] {gtf_list | strg1.gtf.}

Option

-G reference transcript comment information (GTF/GFF3)

-o merge the GTF output file of the transcript (default: stdout)

-m minimum length of merged transcript (default: 50)

-c minimum coverage of merged transcripts (default: 0)

-F the minimum FPKM value of the merged transcript (default: 1.0)

Minimum TPM value of-T merged transcript (default: 1. 0)

-f isoform minimum ratio (default: 0.01)

-g transcripts see GAP length less than threshold merges two transcripts (default: 250)

-I allow intron retention in the merged transcript; by default

-l output transcript name prefix (default: MSTRG)

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