A function to extract pair end reads from the bam file generated with subread functionRaffaele A Calogero
These being read-pairs where either is flagged secondary, supplementary and unmapped. Depending on your environment, you may wish to add concurrency with BWA (-t) and Samtools command (-@). bwa mem -5SP contigs.fasta.gz hic_paired.fastq.gz | \ samtools view -F 0x904 -bS - | \ ...
Samtools (v1.11) [59] was used to examine the mapped files, and raw read values for all of the annotated genes were determined using bedtools multiBamCov v2.30.0 [60]. Non-informative data were removed by filtering the genes with a total expression level less than 20 reads. To execute...
Internally BWA concatenates all reference sequences into one long sequence. A read may be mapped to the junction of two adjacent reference sequences. In this case, BWA-backtrack will flag the read as unmapped (0x4), but you will see position, CIGAR and all the tags. A similar issue may...
Other Options: -a --acceptDupMarks Accept duplicate marks already in input file instead of looking for duplicates in the input. -e --excludeDups Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file. -r --removeDups Remove duplicates reads from all output files. ...