Hi everyone
I am using Bowtie 2 (2.0.0-beta2) to do alignments on the output reads of an Illumina HiSeq 50bp paired-end RNA-seq experiment.
A preliminary analysis indicated that I have some rRNA condamination that is skewing my alignment quality metrics and I would like to get rid of those reads before further processing.
I have tried the --un option in two different ways:
1)As paired-end
bowtie2 -a -x /path1/path1/Scer_rRNA -1 /path2/path2/READS_R1.fastq -2 /path2/path2/READS_R2.fastq --un ./READS_NOrRNA.fastq
2)As single-end
bowtie2 -a -x /path1/path1/Scer_rRNA --un ./READS_NOrRNA.fastq -U /path2/path2/READS_R1.fastq -S /path2/path2/READS_not_R2.sam
(Also note the slight variations on the --un suntax)
In both cases I got the same error :Warning: Could not open read file "./READS_NOrRNA.fastq" for reading; skipping...
Does anyone have any ideas of how I should use the --un option or other ways to do the same thing?
Thank you.
I am using Bowtie 2 (2.0.0-beta2) to do alignments on the output reads of an Illumina HiSeq 50bp paired-end RNA-seq experiment.
A preliminary analysis indicated that I have some rRNA condamination that is skewing my alignment quality metrics and I would like to get rid of those reads before further processing.
I have tried the --un option in two different ways:
1)As paired-end
bowtie2 -a -x /path1/path1/Scer_rRNA -1 /path2/path2/READS_R1.fastq -2 /path2/path2/READS_R2.fastq --un ./READS_NOrRNA.fastq
2)As single-end
bowtie2 -a -x /path1/path1/Scer_rRNA --un ./READS_NOrRNA.fastq -U /path2/path2/READS_R1.fastq -S /path2/path2/READS_not_R2.sam
(Also note the slight variations on the --un suntax)
In both cases I got the same error :Warning: Could not open read file "./READS_NOrRNA.fastq" for reading; skipping...
Does anyone have any ideas of how I should use the --un option or other ways to do the same thing?
Thank you.
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