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Old 10-07-2015, 01:43 PM   #1
graceqy
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Location: New York City

Join Date: Mar 2012
Posts: 14
Default STAR alignment with multiple fq files

I am trying to do RNAseq PE alignment using STAR. It works for one pair of fq files:

$ STAR --runThreadN 30 --genomeDir /srv/STAR_genome/human/ --readFilesIn /../RNA4_1_R1.fastq.gz /../RNA4_1_R2.fastq.gz --readFilesCommand zcat

However, I have multiple fq files for one sample and I need to align them into one sam file. When I tried to align all together, it returns 'Segmentation fault (core dumped)':

$ STAR --runThreadN 30 --genomeDir /../STAR_genome/human/ --readFilesIn /../RNA4_1_R1.fastq.gz /../RNA4_1_R2.fastq.gz /srv/RNA4_2_R1.fastq.gz /../RNA4_2_R2.fastq.gz --readFilesCommand zcat
Segmentation fault (core dumped)

Could STAR deal with multiple pairs? What am I missing, pls?

Last edited by graceqy; 10-07-2015 at 02:05 PM.
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