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STAR alignment error: unrecognized parameter name "genomeType" in input "genomeParameters.txt"

Hello,

I am using STAR to align my RNAseq datasets and I am having this error

EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"
SOLUTION: use correct parameter name (check the manual)

This is my command

module load bioinfo/STAR-2.7.2b
STAR --genomeDir ThuAlb1.1_genomic_index/ --readFilesCommand zcat --readFilesIn T_A_FOIE_S10_L001_R1_001.fastq.gz  T_A_FOIE_S10_L001_R2_001.fastq.gz  --outFilterType BySJout --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate

I am not able to figure out the problem. I am glad if someone help me

Thank you

genometype star alignment mapping rna-seq
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updated by Ram Ram • written by Emy Alade • Emy Alade

2 answers

Has the index been created with a different version of STAR?

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written by ATpoint ATpoint

You're right. I make it with different version.

Thanks

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written by Emy Alade • Emy Alade

GenomeParameters.txt is a file found in your genomeDir. All the files of that type I've checked, and some are quite old, do not have a line that says "genomeType". Perhaps there is a mismatch in the software version used to make the index and the one you are trying to use now.

The cheesy way to fix this would be to simply remove that line from the genomeParameters.txt file.

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written by swbarnes2 swbarnes2

That is interesting because I have this from an index made using v.2.7.4

$ grep genomeType genomeParameters.txt 
genomeType      Full
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written by GenoMax GenoMax

Ah. I usually use 2.7.1, because that's what's compatible with the indices that 10XGenomics makes. And do get errors when trying to use newer versions of STAR with those indices, though it doesn't give me that particular error (it just tells me that the versions are incompatible)

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written by swbarnes2 swbarnes2

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