Hi all,
I am trying to removed Phix reads from my miseq data but I keep on getting
# reads processed: 839305
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 839305 (100.00%)
No alignments
The bowtie command used is - bowtie PhiX_index --sam --al aligned.fq --un unaligned.fq -1 ~/misedata/phixinput/13_S13_L001_R1_001.fastq.out -2 ~/misedata/phixinput/13_S13_L001_R2_001.fastq.out S13.sam
could someone tell me where the problem is?
Thanks,
Joshua
I am trying to removed Phix reads from my miseq data but I keep on getting
# reads processed: 839305
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 839305 (100.00%)
No alignments
The bowtie command used is - bowtie PhiX_index --sam --al aligned.fq --un unaligned.fq -1 ~/misedata/phixinput/13_S13_L001_R1_001.fastq.out -2 ~/misedata/phixinput/13_S13_L001_R2_001.fastq.out S13.sam
could someone tell me where the problem is?
Thanks,
Joshua
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