stringtie | Transcript assembly and quantification for RNA-Seq

by gpertea C++ Version: v2.2.1 License: MIT

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | stringtie Summary

stringtie is a C++ library. stringtie has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

Stringtie employs efficient algorithms for transcript structure recovery and abundance estimation from bulk RNA-Seq reads aligned to a reference genome. It takes as input spliced alignments in coordinate-sorted SAM/BAM/CRAM format and produces a GTF output which consists of assembled transcript structures and their estimated expression levels (FPKM/TPM and base coverage values). For additional StringTie documentation and the latest official source and binary packages please refer to the official website:

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Support

stringtie has a low active ecosystem.

It has 281 star(s) with 76 fork(s). There are 26 watchers for this library.

It had no major release in the last 12 months.

There are 192 open issues and 193 have been closed. On average issues are closed in 70 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of stringtie is v2.2.1

Quality

stringtie has 0 bugs and 0 code smells.

Security

stringtie has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

stringtie code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

stringtie is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

stringtie releases are available to install and integrate.

Installation instructions are not available. Examples and code snippets are available.

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stringtie Key Features

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stringtie Examples and Code Snippets

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Community Discussions

Trending Discussions on stringtie

Find specific words after a match

How to extract the lines based on multiple codes in linux?

Can you help me to resolve the error I am getting after running Stringtie prepDE.py?

Snakemake - Missing MissingInputException in line 20: Missing input files for rule stringt:

Use awk/bash to add 1 to all columns but first

QUESTION

Find specific words after a match

Asked 2021-Dec-19 at 09:00

I have a dataset that looks something like this:

...

ANSWER

Answered 2021-Dec-19 at 09:00

Use:

Source https://stackoverflow.com/questions/70406668

QUESTION

How to extract the lines based on multiple codes in linux?

Asked 2020-Nov-16 at 21:11

I have a sample.txt file like below:

...

ANSWER

Answered 2020-Nov-16 at 21:08

You may use a bracket expression to choose from multiple values:

Source https://stackoverflow.com/questions/64865378

QUESTION

Can you help me to resolve the error I am getting after running Stringtie prepDE.py?

Asked 2020-Oct-27 at 15:19

When I run prepDE.py job exit with the following error. I am using StringTie/2.1.4 with Python/2.7.18. Following is the command I was running (inside ADA cluster)

...

ANSWER

Answered 2020-Oct-27 at 15:19

This is an educated guess based on the error and the documentation linked:

-i INPUT, --input=INPUT, --in=INPUT
– a folder containing all sample sub-directories, or a text file with sample ID and path to its GTF file on each line [default: . ]

Try invoking the script with

Source https://stackoverflow.com/questions/64557330

QUESTION

Snakemake - Missing MissingInputException in line 20: Missing input files for rule stringt:

Asked 2020-Apr-02 at 08:14

I am unsuccessful in running this small snakemake program for StringTie; the dry-run gives an error of MissingInputException for the "rule stringt", I am unable to understand the issue here since the same directory structures works fine for a different snakemake program.

I have already generated the bam files using "hisat2" and is located in the directory : "/alternate_splice/bam_out/" which is stored as "bamdir".

The snakemake should be able to locate the input file since the names and location are appropriate, however it throws an error every time.

I did look at the pervious snakemake related questions, however could not solve this issue. If anyone can help me out here, it would be great!

There are 4 samples: for the wildcards, it takes the list from the directory which has the fastq files

...

ANSWER

Answered 2020-Apr-02 at 08:14

As the input you have a variable called tname which isn't used, and I think it is there by mistake:

Source https://stackoverflow.com/questions/60980819

QUESTION

Use awk/bash to add 1 to all columns but first

Asked 2020-Mar-29 at 15:09

I have a table in which the header is the sample list and the first column is the gene list, and the rest is expression values for each gene in each sample. I want to add a pseudocount of 1 to all values, and I currently do it as such:

...

ANSWER

Answered 2020-Mar-29 at 15:09

awk is great language. Just iterate over fields and increment them.

Source https://stackoverflow.com/questions/60916009

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install stringtie

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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