Hi everyone,
I a newbie in Bowtie2, so I have a question about bowtie2 commands for single and paired-end reads.
I have three paired .fastq files, and two single .fastq files.
When I execute the paired files, I use:
bowtie2 -x index -1 file1.fastq -2 file2.fastq -3 file3.fastq ...
When I execute the paired files, I use:
bowtie2 -x index -U file4.fastq file5.fastq ...
The paired files have different number of reads and lines.
These commands are still running, so I wonder did I use them in a right way?
If not, I would appreciate if you could guide me how to use multiple single and paired-end reads.
Thank you very much,
Natasha
I a newbie in Bowtie2, so I have a question about bowtie2 commands for single and paired-end reads.
I have three paired .fastq files, and two single .fastq files.
When I execute the paired files, I use:
bowtie2 -x index -1 file1.fastq -2 file2.fastq -3 file3.fastq ...
When I execute the paired files, I use:
bowtie2 -x index -U file4.fastq file5.fastq ...
The paired files have different number of reads and lines.
These commands are still running, so I wonder did I use them in a right way?
If not, I would appreciate if you could guide me how to use multiple single and paired-end reads.
Thank you very much,
Natasha
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