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Question: DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
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gravatar for cpsosa0006
6 months ago by
cpsosa00060
USA/Rochester/University of Minnesota Rochester
cpsosa00060 wrote:
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
ADD COMMENTlink modified 6 months ago • written 6 months ago by cpsosa00060

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?

 

ADD REPLYlink written 6 months ago by Alejandro Reyes1.5k
0
gravatar for cpsosa0006
6 months ago by
cpsosa00060
USA/Rochester/University of Minnesota Rochester
cpsosa00060 wrote:

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
ADD COMMENTlink written 6 months ago by cpsosa00060

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?

 

ADD REPLYlink written 6 months ago by Alejandro Reyes1.5k
0
gravatar for cpsosa0006
6 months ago by
cpsosa00060
USA/Rochester/University of Minnesota Rochester
cpsosa00060 wrote:

Hi Alejandro,

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

ADD COMMENTlink written 6 months ago by cpsosa00060

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

ADD REPLYlink written 6 months ago by Alejandro Reyes1.5k
0
gravatar for cpsosa0006
6 months ago by
cpsosa00060
USA/Rochester/University of Minnesota Rochester
cpsosa00060 wrote:
  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 )
ADD COMMENTlink written 6 months ago by cpsosa00060
0
gravatar for cpsosa0006
6 months ago by
cpsosa00060
USA/Rochester/University of Minnesota Rochester
cpsosa00060 wrote:

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.

ADD COMMENTlink written 6 months ago by cpsosa00060

Maybe dropbox or google drive would do the job?

ADD REPLYlink written 6 months ago by Alejandro Reyes1.5k
0
gravatar for cpsosa0006
6 months ago by
cpsosa00060
USA/Rochester/University of Minnesota Rochester
cpsosa00060 wrote:

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 )

ADD COMMENTlink written 6 months ago by cpsosa00060

Sure, alejandro.reyes.ds at gmail 

Alejandro

ADD REPLYlink written 6 months ago by Alejandro Reyes1.5k

Great.  I'll do it right.

ADD REPLYlink written 6 months ago by cpsosa00060

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.

ADD REPLYlink written 6 months ago by cpsosa00060
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