<p>Well, it looks like if you're using Windows for managing files - that's not a good idea - it sorts names of your ballgown folders in alphabetical order while you need it differently. </p>

<p>That is why the one should use Linux - when you're <code>ls -ltr</code> your ballgown folder in Linux it gives you the "right" sequence of folder names to be put inside a ballgown object using pData. </p>

<p>This is what helped me to get rid of this error:</p>

<p>In Linux enter your ballgown folder and do <code>ls -ltr | awk '{print$9}'</code> and you will have the <strong>right</strong> sequence that you have to put inside you <code>.csv</code> file using Notepad++, indicating what's what. Below's my example compared to the above mentioned initial example:</p>

<pre><code>id,state
RNA-CCC_12N_S7_L002,control
RNA-CCC_12T_S8_L002,tube
RNA-CCC_13N_S105_L002,control
RNA-CCC_13T_S106_L002,tube
RNA-CCC_23N_S107_L002,control
RNA-CCC_23T_S108_L002,tube
RNA-CCC_8N_S5_L002,control
RNA-CCC_8T1_S6_L002,tube
</code></pre>

<p>I don't have my error anymore and after </p>

<pre><code>phenodata &lt;- read.csv('my_phenodata_file.csv')
bg = ballgown(dataDir = "ballgown", samplePattern = "RNA-CCC_", pData = phenodata) 
</code></pre>

<p>my results are nicely wrapped</p>

<pre><code>Sat May 02 22:11:57 2020
Sat May 02 22:11:57 2020: Reading linking tables
Sat May 02 22:11:59 2020: Reading intron data files
Sat May 02 22:12:04 2020: Merging intron data
Sat May 02 22:12:06 2020: Reading exon data files
Sat May 02 22:12:14 2020: Merging exon data
Sat May 02 22:12:16 2020: Reading transcript data files
Sat May 02 22:12:20 2020: Merging transcript data
Wrapping up the results
Sat May 02 22:12:22 2020
</code></pre>

<p>The problem is explained here as well</p>

<p><a href="https://www.biostars.org/p/228389/" rel="nofollow noreferrer">https://www.biostars.org/p/228389/</a></p>

<p>Hope this will help anyone</p>

CC BY-SA 4.0
2020-05-02T21:03:22.557Z
Thank you very much @'Dmitrii Trubetskoy' it certainly helps.
M__
CC BY-SA 4.0
2020-05-02T20:27:58.393Z
2020-05-02T20:27:58.393Z
Dmitrii Trubetskoy
<p>I am trying to create a ballgown object, and I would like to set a phenodata information.
For that I do </p>

<pre><code>phenodata &lt;- read.csv('l002.csv')
</code></pre>

<p>and my l002.csv file contains the following info</p>

<pre><code>id,state
RNA-CCC_8N_S5_L002,control
RNA-CCC_8T1_S6_L002,tube
RNA-CCC_12N_S7_L002,control
RNA-CCC_12T_S8_L002,tube
RNA-CCC_13N_S105_L002,control
RNA-CCC_13T_S106_L002,tube
RNA-CCC_23N_S107_L002,control
RNA-CCC_23T_S108_L002,tube
</code></pre>

<p>A ballgown folder contains folders that have exactly the same names, e.g. RNA-CCC_8N_S5_L002, RNA-CCC_8T1_S6_L002, etc...
Then, I use this piece of code for bg object creation</p>

<pre><code>bg = ballgown(dataDir = "ballgown", samplePattern = "RNA-CCC_", pData = phenodata )
</code></pre>

<p>but every time I run it, I have the same error every time:</p>

<pre><code>Error in ballgown(dataDir = "ballgown", samplePattern = "RNA-CCC_", pData = phenodata) : 
  first column of pData does not match the names of the folders containing the ballgown data.
</code></pre>

<p>What can be a problem since first column of pData matches exactly the names of the folders containing the ballgown data.. </p>

<p>If I get rid of phenodata ballgown object creation works, but I need this phenodata for further manipulations.</p>

<rna-seq><stringtie>
Why this ballgown error (first column of pData does not match the names of the folders) comes out
# Why this ballgown error (first column of pData does not match the names of the folders) comes out

(Asked by: username_0 on 2020-05-02)

I am trying to create a ballgown object, and I would like to set a phenodata information.
For that I do 
phenodata <- read.csv('l002.csv')

and my l002.csv file contains the following info
id,state
RNA-CCC_8N_S5_L002,control
RNA-CCC_8T1_S6_L002,tube
RNA-CCC_12N_S7_L002,control
RNA-CCC_12T_S8_L002,tube
RNA-CCC_13N_S105_L002,control
RNA-CCC_13T_S106_L002,tube
RNA-CCC_23N_S107_L002,control
RNA-CCC_23T_S108_L002,tube

A ballgown folder contains folders that have exactly the same names, e.g. RNA-CCC_8N_S5_L002, RNA-CCC_8T1_S6_L002, etc...
Then, I use this piece of code for bg object creation
bg = ballgown(dataDir = "ballgown", samplePattern = "RNA-CCC_", pData = phenodata )

but every time I run it, I have the same error every time:
Error in ballgown(dataDir = "ballgown", samplePattern = "RNA-CCC_", pData = phenodata) : 
  first column of pData does not match the names of the folders containing the ballgown data.

What can be a problem since first column of pData matches exactly the names of the folders containing the ballgown data.. 
If I get rid of phenodata ballgown object creation works, but I need this phenodata for further manipulations.

**Tags:** rna-seq, stringtie

---

## 1 answers

### Answer by username_0 on 2020-05-02. Score: 2

Well, it looks like if you're using Windows for managing files - that's not a good idea - it sorts names of your ballgown folders in alphabetical order while you need it differently. 
That is why the one should use Linux - when you're ls -ltr your ballgown folder in Linux it gives you the "right" sequence of folder names to be put inside a ballgown object using pData. 
This is what helped me to get rid of this error:
In Linux enter your ballgown folder and do ls -ltr | awk '{print$9}' and you will have the right sequence that you have to put inside you .csv file using Notepad++, indicating what's what. Below's my example compared to the above mentioned initial example:
id,state
RNA-CCC_12N_S7_L002,control
RNA-CCC_12T_S8_L002,tube
RNA-CCC_13N_S105_L002,control
RNA-CCC_13T_S106_L002,tube
RNA-CCC_23N_S107_L002,control
RNA-CCC_23T_S108_L002,tube
RNA-CCC_8N_S5_L002,control
RNA-CCC_8T1_S6_L002,tube

I don't have my error anymore and after 
phenodata <- read.csv('my_phenodata_file.csv')
bg = ballgown(dataDir = "ballgown", samplePattern = "RNA-CCC_", pData = phenodata) 

my results are nicely wrapped
Sat May 02 22:11:57 2020
Sat May 02 22:11:57 2020: Reading linking tables
Sat May 02 22:11:59 2020: Reading intron data files
Sat May 02 22:12:04 2020: Merging intron data
Sat May 02 22:12:06 2020: Reading exon data files
Sat May 02 22:12:14 2020: Merging exon data
Sat May 02 22:12:16 2020: Reading transcript data files
Sat May 02 22:12:20 2020: Merging transcript data
Wrapping up the results
Sat May 02 22:12:22 2020

The problem is explained here as well
https://www.biostars.org/p/228389/
Hope this will help anyone

> **Comments:**
> **username_1**: Thank you very much @'Dmitrii Trubetskoy' it certainly helps.  

---

