RSEM: The reference contains no transcripts!

Question

[Eric Wang]

I want to use RSEM tool to finish my job. However, I got some question. Here is the code:

rsem-prepare-reference --gtf /home/dwang/Data/GRCh/Homo_sapiens.GRCh37.68.gtf --star -p 2 ~/Data/UCSC/hg19.fa /Data/Results

There are some errors. I do not know why.

Warning: 197611 transcripts are failed to extract because their chromosome sequences are absent.
0 transcripts are extracted.
The reference contains no transcripts!

I downloaded the annotation data from "ensembl" and the reference genome from UCSC.

[WouterDeCoster]

I edited your title to make it more specific about what you are asking.

[GenoMax]

Django : If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Please do the same for your previous posts as well.

Answer 1

[WouterDeCoster]

I downloaded the annotation data from "ensembl" and the reference genome from UCSC.

Well there's your problem. Use annotation from the same source as your reference genome. Your chromosome identifiers have to match.

[Eric Wang]

Thank you for your answer! I downloaded some SRA data from NCBI. I read its introduction:

Data processing Basecalls performed using bcl2fastq (v2-2.19).
Reads were aligned to hg19 reference using STAR (v2.5.2).
Transcripts were quantified using RSEM (v1.2.30) and the GRCh37.68 gtf annotation file.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_21gene_expression.txt: Normalized expression values provided in a log2 scale.

What is the difference between hg19 and GRCh37?

[WouterDeCoster]

Mainly the chromosome identifiers. The sequence is equal.

[Kristoffer Vitting-Seerup]

Yep. Ensembl mark chromosomes as "1","2" etc while UCSC marks them as "chr1", "chr2" etc.