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This article mainly explains "how to use StringTie". The content in the article is simple and clear, and it is easy to learn and understand. Please follow the editor's train of thought to study and learn how to use StringTie.

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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