diploid option / GeneCounts reads

[marie-christine combes]

Hi Alexander,

I work with STAR for few months. I want to study Allelic Specific Expression of rice F1 hybrids (between cultivated and wild rice species). For this study, diploid option is useful to attribute the reads to h1 or h2 haplotype, thanks for the development of this option.

Now my question : for my project I need count h1 and h2 reads by genes.  Is it possible or is there a strategy to directly count h1 and h2 reads during the mapping step like it’s the possibility without the diploid option ? With --quantMode Genecounts, STAR counts number reads per gene while mapping.

If I write --quantMode Genecounts in mapping command line with genome indexes generated with diploid option, I receive the error message, see below.

My command line : STAR --runThreadN 4 --genomeDir /scratch/combes-STARmapping/Ref-dipl-par-gtf --readFilesIn /scratch/combes-STARmapping/A-D-1_1.CUTADAPT.fastq.gz /scratch/combes-STARmapping/A-D-1_2.CUTADAPT.fastq.gz --readFilesCommand zcat --outFilterMismatchNoverLmax 0.03 --quantMode GeneCounts --sjdbGTFfile /scratch/combes-STARmapping/Gal-oryza_glaberrima_core_3_87_4.chr8.chr.renamed.blastp2.iprsca.gtf --outSAMattributes ha

Error message : Fatal INPUT FILE error, no valid exon lines in the GTF file: /scratch/combes-STARmapping/Gal-oryza_glaberrima_core_3_87_4.chr8.chr.renamed.blastp2.iprsca.gtf

Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.

I understand that in case of diploid option, both the genome sequence and transcript/gene annotations are transformed. In my case genome indexes are generated with the gtf, but at the end the names of fasta and gtf don’t match.

I don’t well understand how use the –genomeTransformOutput option to transform back to the original coordinates and possibly names (of the initial refrence).

Thanks a lot 

Marie