Converting BAM to fastq

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

How to split a single .fastq file of paired-end reads into two separated files?

# extracting reads ending with '/1' or '/2'

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 JVM

bedtools 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