It is possible to extract either the mapped or the unmapped reads from the bam file using samtools.

First, sort the alignment

> samtools sort [input.bam] [output_stub]

sort the alignment

to export unmapped reads from assembly.bam to fastq files (# for paired ends)

> bam2fastq --no-aligned --force --strict -o unmapped#.fq [assembly.bam]

Output will be in unmapped_1.fq and unmapped_2.fq

to export mapped reads from assembly.bam to fastq files (# for paired ends)

> bam2fastq --aligned --force --strict -o mapped#.fq [assembly.bam]

Output will be in mapped_1.fq and unmapped_2.fq

http://seqanswers.com/forums/showthread.php?t=14702

Take a look . I hope it helps

There are several options:

1) Use of Picard Tools: SamToFastq (http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq). If you need a GUI, you always can use Galaxy (http://galaxyproject.org/).

2) Use of a pipe with samtools to get the sam, select the right columns (http://samtools.sourceforge.net/SAM1.pdf) and redirect into a file. In this case something like:

samtools view input.bam | cut -f1,10 | sed 's/^/>/' | sed 's/\t/\n/' > out.fasta

samtools view input.bam | cut -f1,10,11 | sed 's/^/>/' | sed 's/\t/\n/' | sed 's/\t/\n+\n/' > out.fastq

@Reema: The thread you have suggested was discussing about something else. Anyway thanks for the help.

@Aureliano: Thanks for the suggestions. Hope both will work.

It is possible to extract either the mapped or the unmapped reads from the bam file using samtools.

First, sort the alignment

> samtools sort [input.bam] [output_stub]

sort the alignment

to export unmapped reads from assembly.bam to fastq files (# for paired ends)

> bam2fastq --no-aligned --force --strict -o unmapped#.fq [assembly.bam]

Output will be in unmapped_1.fq and unmapped_2.fq

to export mapped reads from assembly.bam to fastq files (# for paired ends)

> bam2fastq --aligned --force --strict -o mapped#.fq [assembly.bam]

Output will be in mapped_1.fq and unmapped_2.fq

Please refer to the following thread on seqanswers which discusses the same. (http://seqanswers.com/forums/showthread.php?s=ff86dc537e51bb13492fecb01098c82b&t=12283)

In addition, it might be a good idea to explore the samtools mpileup option for extracting reads using a BED file, i.e. if you need to extract based on coordinates etc.

Good luck !