Hello,
I have paired end fastq files that were retrieved from two bam files using BamUtil and I would like to merge the respective fastq files. The only issue is that since they come from two bam files that were created using the same original fastq reads, there are many reads which are shared between the two respective files (ie bamfile1_reads_1.fastq has shared reads with bamfile2_reads_1.fastq). Are there any tools that would allow me to merge the files while ensuring that there are no duplicated reads in the merged fastq file?
Thank you!
I have paired end fastq files that were retrieved from two bam files using BamUtil and I would like to merge the respective fastq files. The only issue is that since they come from two bam files that were created using the same original fastq reads, there are many reads which are shared between the two respective files (ie bamfile1_reads_1.fastq has shared reads with bamfile2_reads_1.fastq). Are there any tools that would allow me to merge the files while ensuring that there are no duplicated reads in the merged fastq file?
Thank you!
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