Prepare unmapped reads

Some mapping tools produce partially-mapped reads (i.e. STAR). In case read is mapped to BCR or TCR genes and is partially mapped to V or J gene, such read may be used to assemble full-length CDR3 sequences. Considering only unmapped reads will result in missing such reads.

We offer --bam option to extract reads mapped to BCR/BCR loci and unmapped reads from BAM file and perform immune profiling based on extracted reads.

Given the bam file with mapped and unmapped reads, you can run ImReP using this command.

python imrep.py --bam example/toyExample.bam example/toyExample.cdr3

You can use any existing RNA-Seq aligner. For, example, to map RNA-Seq reads and save mapped and unmapped reads into a single BAM file, use STAR with --outSamUnmapped Within option.