STARdiploid

[marie-christine combes]

Hi Alexander,

Thanks for your attention.

I’m new in computational biology. I already worked a little with STAR. I’m very interested in the new option "STARdiploid" in last STAR to analyse F1 hybrids and parents transcriptomics data.

At the genome generation stage, I introduced  « --genomeTransformVC » and « --genomeTransformVC » as indicated in manual or as I understood. But these parameters seem unrecognized… ? What will I do ? I couldn't find any solutions in the manual.

The command line that I wrote and the answer of STAR.

Thanks a lot

Marie

STAR --runThreadN 4 --runMode genomeGenerate --genomeDir Ref-diploid --genomeSAindexNbases 12 --genomeFastaFiles OglaRS2ADWL02.fa --sjdbGTFtagExonParentTranscript panrefVsIRGSP.wochroms.copies.0.95.chr.gff --genomeTransformVC Chr01.F4.vcf --genomeTransformType Diploid

EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeTransformVC" in input "Command-Line-Initial"

SOLUTION: use correct parameter name (check the manual)

[marie-christine combes]

Hi Alexander,

For improving of STAR manual, the problem comes from a typing error : F is missing in the command "--genomeTransformVC" p21 part 14 STARdiploid of manual 2.7.11a. With "--genomeTransformVCF" is possible to map of course.

Best Marie

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