Run STAR with 4 fastq files, ERROR
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4.5 years ago

I recently have a problem when I run STAR for the RNAseq alignment. I have 4 fastq files, when I put all into the script and the program indicates like"EXITING: because of fatal INPUT ERROR: number of input files for mate1: 4 is not equal to that for mate2: 1 Make sure that the number of files in --readFilesIn is the same for both mates"

And my script is STAR --genomeDir /Users/Shared/reference/STAR_hg19 --readFilesCommand gunzip -c --readFilesIn PCa10_S6_L001_R1_001.fastq.gz,PCa10_S7_L001_R1_001.fastq.gz,PCa10_S6_L001_R2_001.fastq.gz, PCa10_S7_L001_R2_001.fastq.gz --outFileNamePrefix PCa10_ --runThreadN 14 --outBAMsortingThreadN 4 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMtype BAM SortedByCoordinate

What is the problem?

RNA-Seq • 7.4k views
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Of course! Thank you so much

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4.5 years ago
GenoMax 102k

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 PCa10_S6_L001_R1_001.fastq.gz,PCa10_S7_L001_R1_001.fastq.gz PCa10_S6_L001_R2_001.fastq.gz,PCa10_S7_L001_R2_001.fastq.gz
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It works. Thank you so much and happy new year!

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Please accept an answer when it answers your question; this helps the entire community. In this case I did it for you.

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