SeqPlots error: chrx not found in BSgenome.Hsapiens.UCSC.hg19
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@karmellahaynes-11317
Last seen 4.7 years ago

Hello community,

I am running SeqPlots via Bioconductor in R, via a browser-based interface. I uploaded my wig file without any issues. When I tried to upload my BED file of 23245 genes I got the following error.

Chromosome names provided in the file does not match ones defined in reference genome. 
INPUT: [chrx]
GENOME: [chr1, chr2, chr3, chr4, chr5, ...]

I looked for other reference genomes at the Bioconductor website, but BSgenome.Hsapiens.UCSC.hg19 seems to be the only appropriate one (genome version hg19). Is chromosome X not included in BSgenome.Hsapiens.UCSC.hg19?

Thank you for your help.

seqplots bed file chromosome error • 474 views
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Follow-on question: Is there a command in R that I can use to list the all chromosome ID's associated within a particular reference genome? I went to the documentation page for BSgenome.Hsapiens.UCSC.hg19 and could not find any useful information.

http://www.bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html

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@james-w-macdonald-5106
Last seen 7 hours ago
United States

You can look this up using the GenomeInfoDb package.

> library(GenomeInfoDb)

> genomeStyles("Homo sapiens")
   circular  auto   sex NCBI  UCSC dbSNP Ensembl
1     FALSE  TRUE FALSE    1  chr1   ch1       1
2     FALSE  TRUE FALSE    2  chr2   ch2       2
3     FALSE  TRUE FALSE    3  chr3   ch3       3
4     FALSE  TRUE FALSE    4  chr4   ch4       4
5     FALSE  TRUE FALSE    5  chr5   ch5       5
6     FALSE  TRUE FALSE    6  chr6   ch6       6
7     FALSE  TRUE FALSE    7  chr7   ch7       7
8     FALSE  TRUE FALSE    8  chr8   ch8       8
9     FALSE  TRUE FALSE    9  chr9   ch9       9
10    FALSE  TRUE FALSE   10 chr10  ch10      10
11    FALSE  TRUE FALSE   11 chr11  ch11      11
12    FALSE  TRUE FALSE   12 chr12  ch12      12
13    FALSE  TRUE FALSE   13 chr13  ch13      13
14    FALSE  TRUE FALSE   14 chr14  ch14      14
15    FALSE  TRUE FALSE   15 chr15  ch15      15
16    FALSE  TRUE FALSE   16 chr16  ch16      16
17    FALSE  TRUE FALSE   17 chr17  ch17      17
18    FALSE  TRUE FALSE   18 chr18  ch18      18
19    FALSE  TRUE FALSE   19 chr19  ch19      19
20    FALSE  TRUE FALSE   20 chr20  ch20      20
21    FALSE  TRUE FALSE   21 chr21  ch21      21
22    FALSE  TRUE FALSE   22 chr22  ch22      22
23    FALSE FALSE  TRUE    X  chrX   chX       X
24    FALSE FALSE  TRUE    Y  chrY   chY       Y
25     TRUE FALSE FALSE   MT  chrM  chMT      MT

 

To answer your original question, yes there is a chromosome X in the BSGenome package you reference, but it's chrX, not chrx. R is case-sensitive, so those are different.

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Thank you! I used your feedback to fix the BED file. I corrected the case on chrX and deleted genes annotated with "extra" chromosome information (e.g. chr6_ssto_hap7). The upload was successful.

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