<p>Ok, I figured it out already, it's and old issue I come accross every now and then. The original bed file lists the chromosomes as chr1,chr2,...,chrX whereas my bam files uses 1,2,...,X</p>

<p>I fixed the bed file like this (python3):</p>

<pre><code>import pandas as pd
bedFile = '/hg38_Gencode_V28.bed'
bedFile = pd.read_csv(bedFile, sep='\t', header=None)
bedFile[0] = [value.strip('chr') for value in bedFile[0]]
newBedFile = 'hg38_Gencode_V28_reformatted.bed'
bedFile.to_csv(newBedFile, sep='\t', header=None, index=None)
</code></pre>

<p>And now read_distribution.py works.</p>

CC BY-SA 4.0
2019-02-11T09:41:50.260Z
You can also use chromosome mappings provided by @dpryan72 here: https://github.com/dpryan79/ChromosomeMappings
Siddharth
CC BY-SA 4.0
2019-02-08T15:48:29.890Z
2019-02-08T15:48:29.890Z
Freek
<p>I frequently make use of <a href="http://rseqc.sourceforge.net/" rel="nofollow noreferrer">RSeQC</a>, I used to use it with my own bed file, generated using gtf2bed, but now I thought I'd use the one provided by RSeQC themselves from <a href="https://sourceforge.net/projects/rseqc/files/BED/Human_Homo_sapiens/" rel="nofollow noreferrer">here</a>, I got the file hg38_Gencode_V28.bed.gz, when looking at it with IGV it looks similar to my self generated bedfile however, read_distribution.py (a script in RSeQC), does not report any reads in any of the categories (CDS_exons, Introns, etc).</p>
<p>Any idea why?</p>
<p>Edit: I see that my own bed file (from the GTF) had ENST identifiers like this ENST00000466557 whereas the file from RSeQC supplies them like ENST00000611746.1 (with decimals) that seems to be the only difference as far as I can see.</p>

<rna-seq><qc><rseqc>
RSeQC provided bedfile does not work with read_distribution.py
# RSeQC provided bedfile does not work with read_distribution.py

(Asked by: username_0 on 2019-02-08)

I frequently make use of [RSeQC](http://rseqc.sourceforge.net/), I used to use it with my own bed file, generated using gtf2bed, but now I thought I'd use the one provided by RSeQC themselves from [here](https://sourceforge.net/projects/rseqc/files/BED/Human_Homo_sapiens/), I got the file hg38\_Gencode\_V28.bed.gz, when looking at it with IGV it looks similar to my self generated bedfile however, read\_distribution.py (a script in RSeQC), does not report any reads in any of the categories (CDS\_exons, Introns, etc).

Any idea why?

Edit: I see that my own bed file (from the GTF) had ENST identifiers like this ENST00000466557 whereas the file from RSeQC supplies them like ENST00000611746.1 (with decimals) that seems to be the only difference as far as I can see.

**Tags:** rna-seq, qc, rseqc

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## 1 answers

### Answer by username_0 on 2019-02-08. Score: 2

Ok, I figured it out already, it's and old issue I come accross every now and then. The original bed file lists the chromosomes as chr1,chr2,...,chrX whereas my bam files uses 1,2,...,X
I fixed the bed file like this (python3):
import pandas as pd
bedFile = '/hg38_Gencode_V28.bed'
bedFile = pd.read_csv(bedFile, sep='\t', header=None)
bedFile[0] = [value.strip('chr') for value in bedFile[0]]
newBedFile = 'hg38_Gencode_V28_reformatted.bed'
bedFile.to_csv(newBedFile, sep='\t', header=None, index=None)

And now read_distribution.py works.

> **Comments:**
> **username_1**: You can also use chromosome mappings provided by @dpryan72 here: https://github.com/dpryan79/ChromosomeMappings  

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