Skip to content

Commit

Permalink
update
Browse files Browse the repository at this point in the history
  • Loading branch information
Sherking committed Sep 23, 2019
1 parent 7557a72 commit 4b6dd43
Show file tree
Hide file tree
Showing 2 changed files with 43 additions and 42 deletions.
75 changes: 38 additions & 37 deletions Implementation.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,15 +24,15 @@
----
<!-- /TOC -->
# **Introduction**
The **RiboMiner** is a python package used for downstream analysis of ribosome profiling data. This package has four function parts:
The **[RiboMiner](https://github.com/xryanglab/RiboMiner)** is a python toolset for mining multi-dimensional features of the translatome with ribosome profiling data. This package has four function parts:


+ **Quality Control (QC)**: Quality control for ribosome profiling data, containing periodicity checking, reads distribution among different reading frames,length distribution of ribosome footprints and DNA contaminations.
+ **Metagene Analysis (MA)**: Metagene analysis among different samples to find possible ribosome stalling events.
+ **Feature Analysis (FA)**: Feature analysis among different gene sets identified in MA step to explain the possible ribosome stalling.
+ **Enrichment Analysis (EA)**: Enrichment analysis to find possible co-translation events.

In this file, we will show you how to use our **RiboMiner** based on some published datasets.
In this file, we will show you how to use our **[RiboMiner](https://github.com/xryanglab/RiboMiner)** based on some published datasets.

# **Data preparation (DP)**

Expand Down Expand Up @@ -424,38 +424,39 @@ EnrichmentAnalysisForSingleTrans -i all_codon_ratio.txt.txt -s ARC1 -o ARC1 -c <
```
![EA.png-284.3kB][31]
**Figure 6: The results of Enrichment Analysis**. **A.** Engagement of nascent ARC1 (top), GUS1 (bottom) by C-terminally tagged MetRS. **B.** Engagement of nascent ARC1 (top), MES1 (bottom) by C-terminally tagged GluRS.
[1]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png
[2]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png
[3]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png
[4]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png
[5]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png
[6]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png
[7]: http://static.zybuluo.com/sherking/fhl1830e4ymca16oezezn4eg/QC.png
[8]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png
[9]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png
[10]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png
[11]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png
[12]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png
[13]: http://static.zybuluo.com/sherking/2pi6e3rq2sr052lqbqxjs3so/MA.png
[14]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png
[15]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png
[16]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png
[17]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png
[18]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png
[19]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png
[20]: http://static.zybuluo.com/sherking/l9cjetv127vexf8dc6pwth5q/AADensity.png
[21]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png
[22]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png
[23]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png
[24]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png
[25]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png
[26]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png
[27]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png
[28]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png
[29]: http://static.zybuluo.com/sherking/vpx5pimueh9w3d7gr2o5hppw/triAADensity.png
[30]: http://static.zybuluo.com/sherking/1j4txn5zno1pex79c5ja1bqx/CAItAI.png
[31]: http://static.zybuluo.com/sherking/jjy5h149wmn9cudfbpijffwy/EA.png
**Figure 6: The results of Enrichment Analysis**. **A.** Engagement of nascent ARC1 (top), GUS1 (bottom) by C-terminally tagged MetRS. **B.** Engagement of nascent ARC1 (top), MES1 (bottom) by C-terminally tagged GluRS. The red dotted lines represent twofold threshold.
[1]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png
[2]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png
[3]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png
[4]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png
[5]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png
[6]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png
[7]: http://static.zybuluo.com/sherking/4wuu4omw1r3edhnhxoalot9q/QC2.png
[8]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png
[9]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png
[10]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png
[11]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png
[12]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png
[13]: http://static.zybuluo.com/sherking/v59lhdcvwk57fya119a4r3rq/MA.png
[14]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png
[15]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png
[16]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png
[17]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png
[18]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png
[19]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png
[20]: http://static.zybuluo.com/sherking/rl0wsq9zbrgnjg5f8alz00p5/AADensity.png
[21]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png
[22]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png
[23]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png
[24]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png
[25]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png
[26]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png
[27]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png
[28]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png
[29]: http://static.zybuluo.com/sherking/r1oq3on8woelch6m307te3o4/triAADensity.png
[30]: http://static.zybuluo.com/sherking/r877xvlk0zyf0q6mfelxzbiv/CAItAI.png
[31]: http://static.zybuluo.com/sherking/ae5qqlvl8x8nfr157vy7gpgu/EA.png
10 changes: 5 additions & 5 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@

---
# **Introduction**
The **RiboMiner** is a python package used for downstream analysis of ribosome profiling data. This package has four function parts:
The **RiboMiner** is a python toolset for mining multi-dimensional features of the translatome with ribosome profiling data. This package has four function parts:


+ **Quality Control (QC)**: Quality control for ribosome profiling data, containing periodicity checking, reads distribution among different reading frames,length distribution of ribosome footprints and DNA contaminations.
Expand All @@ -44,7 +44,7 @@ The **RiboMiner** is a python package used for downstream analysis of ribosome p

# **Installation**

**[RiboMiner](https://github.com/sherkinglee/RiboMiner)** can be installed like any other Python packages. Here are some popular ways:
**[RiboMiner](https://github.com/xryanglab/RiboMiner)** can be installed like any other Python packages. Here are some popular ways:

+ Install via pypi:
```
Expand All @@ -53,7 +53,7 @@ pip install RiboMiner
+ Install from source:

```
git clone https://github.com/sherkinglee/RiboMiner.git
git clone https://github.com/xryanglab/RiboMiner.git
cd RiboMiner
python setup.py install
```
Expand All @@ -64,7 +64,7 @@ python setup.py install

## **Data preparation (DP)**

The analysis based on this package need some transcript sequences and annotation file. Before starting the analysis, we need to prepare those files ahead of time. However, the basic annotation file such genome FASTA file, GTF file for annotation which may be used for mapping need to be downloaded by user themselves.
The analysis based on this package need some transcript sequences and annotation file. Before starting the analysis, we need to prepare those files ahead of time. However, the basic annotation file such genome FASTA file, GTF file for annotation which may be used for mapping need to be downloaded by user themselves from [ensemble](http://www.ensembl.org/info/data/ftp/index.html).

+ **Prepare sequences and annotaiton files on transcriptome level.**

Expand Down Expand Up @@ -469,4 +469,4 @@ EnrichmentAnalysisForSingleTrans -i <output_prefix_codon_ratio.txt> -s <transcri
where the *output_prefix_codon_ratio.txt* was generated by *EnrichmentAnalysis* in **Step 3**; *transcript_name* is the single transcript you are interested in, and either transcript id or gene name or gene id for that transcript was required.This step would generate a plot file with *pdf* format. And if you set *-S* rather than *-s* with a transcript list file input, the output file would be a *pdf* file containing plots for each transcript.
# **Implementation**
Details for mplementation, please refer to [Implementation](https://github.com/sherkinglee/RiboMiner/blob/master/Implementation.md).
Details for mplementation, please refer to [Implementation](https://github.com/xryanglab/RiboMiner/blob/master/Implementation.md).

0 comments on commit 4b6dd43

Please sign in to comment.