Hello,
I have just recently started working with Bowtie and am having problems with outputting the information that I want. I have paired end reads that are in fastq.gz format and I have been trying to use the —al and —un options. The files are created, but there are not data in either of them. Also, the manual suggests that 2 files would be output for each of the used and unused reads (e.g usedreads_1.fq usedreads_2.fq) given that I am working with paired end data.
Here’s what I am trying:
bowtie2 --un UnusedReads.fq --al UsedReads.fq -x reference.fa -1 pairedendFWD.fastq.gz -2 pairedendREV.fastq.gz -S output.sam
Thanks for any help!
I have just recently started working with Bowtie and am having problems with outputting the information that I want. I have paired end reads that are in fastq.gz format and I have been trying to use the —al and —un options. The files are created, but there are not data in either of them. Also, the manual suggests that 2 files would be output for each of the used and unused reads (e.g usedreads_1.fq usedreads_2.fq) given that I am working with paired end data.
Here’s what I am trying:
bowtie2 --un UnusedReads.fq --al UsedReads.fq -x reference.fa -1 pairedendFWD.fastq.gz -2 pairedendREV.fastq.gz -S output.sam
Thanks for any help!
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