STAR Index output: exonGeTrInfo.tab

Question

[cgias]

Hello everyone,

I'm new at bioinformatics and I'm sorry if my question is too basic, I've searched a lot but none of the topics have helped me.

I got my genome index trought STAR using the following code:

STAR --runMode genomeGenerate \ 
  --runThreadN 6 \
  --genomeDir /home/carolgs/Cpapaya/STARindex2 \
  --genomeFastaFiles Cpapaya_113_r.Dec2008.fa \
  --sjdbGTFtagExonParentTranscript Cpapaya_113_ASGPBv0.4.gene.gff3  \
  --sjdbGTFfeatureExon exon \
  --outSAMtype BAM SortedByCoordinate \
  --genomeChrBinNbits 18

It worked fine, but then I run:

STAR --quantMode GeneCounts --runThreadN ${PBS_NUM_PPN} \
  --outSAMtype BAM SortedByCoordinate \
  --readFilesIn filtered_PE1.fastq filtered_PE2.fastq \
  --genomeDir /home/carolgs/Cpapaya/STARindex2 \
  --outFilterMultimapNmax 5

And the error message I got was:

Transcriptome.cpp:51:Transcriptome: exiting because of INPUT FILE error: could not open input file /home/carolgs/Cpapaya/STARindex2/exonGeTrInfo.tab Solution: check that the file exists and you have read permission for this file SOLUTION: utilize --sjdbGTFfile /path/to/annotantions.gtf option at the genome generation step or mapping step

I can't use --sjdbGTFfile /path/to/annotantions.gtf because my annotation file is .gff3 and doesn't have exons feature

How can I get this exonGeTrInfo.tab file in the index?

Thanks in advance,

[yueli7]

The file of "exonGeTrInfo.tab" should generate automatically when you make index (the first command line).

I can not see clearly of your first command.

It would be helpful if you copy all the command and process.

[cgias]

My first command is

STAR --runMode genomeGenerate \ --runThreadN 6 \ --genomeDir /home/carolgs/Cpapaya/STARindex2 \ --genomeFastaFiles Cpapaya_113_r.Dec2008.fa \ --sjdbGTFtagExonParentTranscript Cpapaya_113_ASGPBv0.4.gene.gff3 \ --sjdbGTFfeatureExon exon \ --outSAMtype BAM SortedByCoordinate \ --genomeChrBinNbits 18

All I did was creating the index and then trying to map and count the genome with the second command

STAR --quantMode GeneCounts --runThreadN ${PBS_NUM_PPN} --outSAMtype BAM SortedByCoordinate \ --readFilesIn filtered_PE1.fastq filtered_PE2.fastq \ --genomeDir /home/carolgs/Cpapaya/STARindex2 \ --outFilterMultimapNmax 5

Answer 1

[h.mon]

Contrary to what you think, your STAR --runMode genomeGenerate is missing --sjdbGTFfile Cpapaya_113_ASGPBv0.4.gene.gff3 (which implies --sjdbGTFtagExonParentTranscript Cpapaya_113_ASGPBv0.4.gene.gff3 is an incorrect option).

You do not need --outSAMtype BAM SortedByCoordinate to generate the genome. And I am not sure what effect --sjdbGTFfeatureExon exon will have if your gff3 file does not contain exon information.

Phytozome has an annotation including exon information: "Cpapaya_113_ASGPBv0.4.gene_exons.gff3". You will have to sign up to download it, though. Alex Dobin (STAR author) recommends converting gff3 to gtf with gffread, or read here, here and here to set your STAR --runMode genomeGenerate parameters correctly.

[cgias]

I made the index using this ...gene_exon.gff3 and it worked! I finally have my exonGeTrInfo.tab file.

STAR --runMode genomeGenerate --runThreadN 6 \ --genomeDir /home/carolgs/Cpapaya/STARindex2 \ --genomeFastaFiles Cpapaya_113_r.Dec2008.fa \ --sjdbGTFfile Cpapaya_113_ASGPBv0.4.gene_exons.gff3 \ --genomeChrBinNbits 18

Then I ran STAR :

STAR --quantMode GeneCounts --runThreadN ${PBS_NUM_PPN}\ --outSAMtype BAM SortedByCoordinate \ --readFilesIn filtered_PE1.fastq filtered_PE2.fastq \ --genomeDir /home/carolgs/Cpapaya/STARindex2 \ --outFilterMultimapNmax 5

It apparently worked, I'm not sure how to interpret all the outputs but I'm gonna find out.

Thanks a lot!