Error while aligning with STAR
Hi,
When I try to run this command. Note that I change working directory to directory containing fast files
STAR --genomeDir /N/slate/ogaafer/mm10_index --runThreadN 8 \
--readFilesIn SRR8278856_1.fastq,SRR8278856_2.fastq SRR8278857_1.fastq,SRR8278857_2.fastq SRR8278859_1.fastq,SRR8278859_2.fastq \
--outSAMattrRGline ID:cont1 , ID:cont2 , ID:cont3 \
--outSAMtype BAM SortedByCoordinate --outSAMunmapped Within \
--outSAMattributes Standard
I get this error
EXITING: because of fatal INPUT ERROR: number of input read files: 2 does not agree with number of read group RG entries: 3
Make sure that the number of RG lines in --outSAMattrRGline is equal to either 1, or the number of input read files in --readFilesIn
1 answer
From Run STAR with 4 fastq files, ERROR (and now I will plagiarize):
You are not using correct separation of the file names. Separate group of paired-end mates by a space and multiple R1/R2 files by commas. Try:
--readFilesIn SRR8278856_1.fastq,SRR8278857_1.fastq,SRR8278859_1.fastq SRR8278856_2.fastq,SRR8278857_2.fastq,SRR8278859_2.fastq
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