Help requiring DEXSeq in R

Question

[achanda]

Hi, community,

I am in a small pickle. I am trying to perform DEXseq on RNA-seq data of several samples. However, when I run the code I get stuck with it.

Error in FUN(X[[i]], ...) : subscript out of bounds

Here is the full steps I am running.

dds <- DEXSeqDataSetFromHTSeq(countFiles = HO120_file_paths,
                              sampleData = HO120_sample_info,
                              design = ~ sample + exon + condition:exon,
                              flattenedfile = flattened_file)

I have checked the naming conventions, paths, everything but still getting the error. The count files in question just have 2 columns, exon_ID and counts. They were generated using STAR aligner followed by HTSeq. The flattened file is the one I generated from gencode hg38 gtf file with dexseq.

I would really appreciate any insights you may have on this error. Please ask me for information if need be.

Answer 1

[Trivas]

Try regenerating your flattenedFile with the same GTF that you used to generate your STAR index. See other forum post for similar issue https://support.bioconductor.org/p/89407/