DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
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cpsosa0006 • 0
@cpsosa0006-12645
Last seen 5.6 years ago
USA/Rochester/University of Minnesota R…
Hello,
I am trying to use DEXSeq for the first time and I am encountering this error.  I am closely following this paper: "Inferring differential exon usage in RNA-Seq data with the DEXSeq package "  I am using my own data.

The files correspond to:

countFiles = 37 samples with counts generated as suggested in the paper.

flattenedfile = GTF annotation file as provided by Illumina in iGenomes.

Could the problem be related to the very large GTF file?

Thanks

> dxd = DEXSeqDataSetFromHTSeq(
+     countFiles,
+     sampleData=sampleTable,
+     design= ~ sample + exon + condition:exon,
+     flattenedfile=flattenedFile )

Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq • 2.2k views
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Maybe the problem is with the gtf file, are you giving as input the gtf produced by the dexseq_prepare_annotation.py file or the one provided by iGenomes?

 

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cpsosa0006 • 0
@cpsosa0006-12645
Last seen 5.6 years ago
USA/Rochester/University of Minnesota R…

I flattened the GTF file via that py script as specified in that paper.  I used the same flattened file when running HTSeq.

This is from the paper:

python /path/to/library/DEXSeq/python_scripts/dexseq_count.py
             Dmel.BDGP5.25.62.DEXSeq.chr.gff untreated1.sam untreated1fb.txt
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I see, sorry I am finding it hard to track the problem. Can you verify that all the count files have the same number of lines? Also, can you check whether the number of lines containing "exonic_part" in the third column of the flattened gtf file correspond to the number of lines from the count files?

 

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cpsosa0006 • 0
@cpsosa0006-12645
Last seen 5.6 years ago
USA/Rochester/University of Minnesota R…

Hi Alejandro,

I'll proceed to check that.  I'll let you know.  Thanks

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OK, if the numbers are consistent and still does not work, maybe the easiest is if you send me a subset of the files such that I can try to reproduce the error message. Alejandro

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cpsosa0006 • 0
@cpsosa0006-12645
Last seen 5.6 years ago
USA/Rochester/University of Minnesota R…
  1. All the count files have exactly the same number of lines as reported by "wc -l"  A total of 66028.
  2. This is the command I used to create the gff file: python /data5/bsi/adhoc/s200555.R-infrastructure/install/R-3.2.3/new/DEXSeq/python_scripts/dexseq_prepare_annotation.py genes.gtf genes.gff
  3. I did not see this number "66028" in the gff file.  Here are just the top lines of the file:

    KN196472.1    dexseq_prepare_annotation.py    aggregate_gene    14223    14535    .    -    .    gene_id "ENSG00000281764.1"

    KN196472.1    dexseq_prepare_annotation.py    exonic_part    14223    14535    .    -    .    transcripts "ENST00000630776.1"; exonic_part_number "001"; gene_id "ENSG00000281764.1"

    KN196472.1    dexseq_prepare_annotation.py    aggregate_gene    81784    81917    .    +    .    gene_id "ENSG00000281299.1"

    KN196472.1    dexseq_prepare_annotation.py    exonic_part    81784    81917    .    +    .    transcripts "ENST00000626225.1"; exonic_part_number "001"; gene_id "ENSG00000281299.1"

    KN196472.1    dexseq_prepare_annotation.py    aggregate_gene    111604    133487    .    +    .    gene_id "ENSG00000281518.2"

  4. Finally, the original gtf file is the annotation file provided in iGenomes and it is located here in the iGenomes directory ( Homo_sapiens/NCBI/GRCh38/Annotation/Genes.gencode )
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cpsosa0006 • 0
@cpsosa0006-12645
Last seen 5.6 years ago
USA/Rochester/University of Minnesota R…

How can I make files available?  Is there an ftp location where I can put the files?  I believe that I can ftp but I need to check with firewall restrictions.

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Maybe dropbox or google drive would do the job?

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cpsosa0006 • 0
@cpsosa0006-12645
Last seen 5.6 years ago
USA/Rochester/University of Minnesota R…

Hi Alejandro,

I have uploaded the files in dropbox.  I'll need your e-mail address to share that folder with you.

This is the command I used to create the sampleTable.

sampleTable = data.frame(
  row.names = c(  "ME26501", "ME26502", "ME26503", "ME26504", "ME26505", "ME26506", "ME26507", "ME26508", "ME26509", "ME26510", "ME26511", "ME26512", "ME26513", "ME26514", "ME26515", "ME26516", "ME26517", "ME26518", "ME26519", "ME26520", "ME26521", "ME26522", "ME26523", "ME26524", "ME26525", "ME26526", "ME26527", "ME26528", "ME26529", "ME26530", "ME26531", "ME26532", "ME26533", "ME26534", "ME26535", "ME26536", "ME26537" ),
  condition = c(  "yes", "yes", "yes", "yes", "yes", "yes", "yes", "yes", "yes", "yes", "yes", "yes", "yes", "yes", "yes", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no", "no" ),
  libType = c(  "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end" ) )

and this is for dxd:

dxd = DEXSeqDataSetFromHTSeq(
  countFiles,
  sampleData=sampleTable,
  design= ~ sample + exon + condition:exon,
  flattenedfile=flattenedFile )

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Sure, alejandro.reyes.ds at gmail 

Alejandro

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Dear Alejandro, I have same problem. Kindly, how did you overcome this error ?

Best

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same problem here :(

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Great.  I'll do it right.

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OK. I sent you an e-mail (location of the folder) and the folder is shared.  Please let me know if you do NOT get my e-mail.

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