Run STAR with 4 fastq files, ERROR

Question

[shangqianwang]

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?

[shangqianwang]

Of course! Thank you so much

Answer 1

[GenoMax]

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

[shangqianwang]

It works. Thank you so much and happy new year!

[Brian Bushnell]

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