SAMtools# sort paired read alignment .bam file (sort by name -n) samtools sort -n SAMPLE.bam -o SAMPLE_sorted.bam # save fastq reads in separate R1 and R2 files samtools fastq -@ 8 SAMPLE_sorted.bam \ -1 SAMPLE_R1.fastq.gz \ -2 SAMPLE_R2.fastq.gz \ -0 /dev/null -s /dev/null -n # Using bam2fq
samtools bam2fq SAMPLE.bam > SAMPLE.fastq
paired-end reads: '/1' or '/2' is added to the end of read names http://www.htslib.org/doc/samtools.html cat SAMPLE.fastq | grep '^@.*/1$' -A 3 --no-group-separator > SAMPLE_r1.fastq cat SAMPLE.fastq | grep '^@.*/2$' -A 3 --no-group-separator > SAMPLE_r2.fastq converting a SAMPLE.bam file into paired end SAMPLE_r1.fastq and SAMPLE_r2.fastq files
java -Xmx2g -jar Picard/SamToFastq.jar I=SAMPLE.bam F=SAMPLE_r1.fastq F2=SAMPLE_r2.fastq F2 to get two files for paired-end reads (R1 and R2) -Xmx2g allows a maximum use of 2GB memory for the JVMhttp://broadinstitute.github.io/picard/command-line-overview.html#SamToFastq http://manpages.ubuntu.com/manpages/quantal/man1/bam2fastx.1.html Bedtoolsbedtools bamtofastq -i input.bam -fq output.fastq paired-end reads: samtools sort -n input.bam -o input_sorted.bam # sort reads by identifier-name (-n)bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq http://bedtools.readthedocs.org/en/latest/content/tools/bamtofastq.html |