Extract the mapped contig sequences from SAM/BAM file

Question

[BDK_compbio]

I have a sam/bam file that contains the mapping of long reads with assembled contigs from short reads. Because of low coverage of long reads, I have 80% of the contigs that are not mapped to s single read. I would like to extract the contigs (with nucleotide sequence) that have at least one mapped reads. How could I do it quickly using my SAM/BAM files? Also, I would like to extract the sequences of a particular contiguous and its mapped long read sequences. Any help would be appreciated.

Answer 1

[vmicrobio]

you may extract your mapped reads using samtools then bamtools to get a fastq and a sed to get your result in fasta format

samtools view -F4 -b in.bam > mapped-out.bam

bamtools convert -in mapped-out.bam -format fastq > mapped-out.fastq

sed -n '1~4s/^@/>/p;2~4p' mapped-out.fastq > mapped-out.fasta