Hi,
I am working on bam files, and need to extract only the paired reads and output them in 2 fastq files (I'm working on a Mac's Terminal).
I extract the paired reads with samtools view:
$ samtools view -f1 -b /Input_file.bam > /pair_reads_file.bam
I then use the picard tools 1.87 version's SamToFastq to create the fastq file:
@ java -jar -Xmx2g /SamToFastq.jar I=/pair_reads_file.bam F=/Output.read1.fastq F2=/Output.read2.fastq VALIDATION_STRINGENCY=SILENT
The process creates two fastq files that should be of the same size, which I need for the following analysis. This works with most of my datas (1000 Genome data), but in some rare cases, it creates different size fastq. The number of reads in the 2 fastq files is the same, but one is bigger than the other (around 5% bigger).
Any suggestion on why is this happening?
Thank you in advance!
I am working on bam files, and need to extract only the paired reads and output them in 2 fastq files (I'm working on a Mac's Terminal).
I extract the paired reads with samtools view:
$ samtools view -f1 -b /Input_file.bam > /pair_reads_file.bam
I then use the picard tools 1.87 version's SamToFastq to create the fastq file:
@ java -jar -Xmx2g /SamToFastq.jar I=/pair_reads_file.bam F=/Output.read1.fastq F2=/Output.read2.fastq VALIDATION_STRINGENCY=SILENT
The process creates two fastq files that should be of the same size, which I need for the following analysis. This works with most of my datas (1000 Genome data), but in some rare cases, it creates different size fastq. The number of reads in the 2 fastq files is the same, but one is bigger than the other (around 5% bigger).
Any suggestion on why is this happening?
Thank you in advance!
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