I use alfred to extract reads aligned to a particular region from a bam file. My bam file is derived from Illumina paired-end read data. Currently I can extract all reads mapping to a particular location, which is more of less what one would see in IGV individual read view. However, IGV has the option to view reads as paired and I would really like to be able to extract the reads from a bam file as such. Would it be possible to provide that option in alfred? It would greatly help me and maybe some others as well. Thanks in advance.
For the consensus subcommand this would not work because reads need to overlap the input position. alfred computes a classical multiple sequence alignment around that input position.
I use alfred to extract reads aligned to a particular region from a bam file. My bam file is derived from Illumina paired-end read data. Currently I can extract all reads mapping to a particular location, which is more of less what one would see in IGV individual read view. However, IGV has the option to view reads as paired and I would really like to be able to extract the reads from a bam file as such. Would it be possible to provide that option in alfred? It would greatly help me and maybe some others as well. Thanks in advance.