I used simpleaf to run my analysis, since I have only available transcriptomes and no genomes. For indexing I cat the fasta files and I created a single referenmce. Then at quant I used my fastq files containing info from both species (invertebrates). SInce 10X is using coloured beads to demultiplex and I did not found any info on how to demultiplex via simpleaf, I simply created a gene2species dictionary in order to do so. My question is. if some sequences are very similar, how does simpleaf quant assign them? Does it discard them? I cannot see any qc report about reads so I am wondering.
I used simpleaf to run my analysis, since I have only available transcriptomes and no genomes. For indexing I cat the fasta files and I created a single referenmce. Then at quant I used my fastq files containing info from both species (invertebrates). SInce 10X is using coloured beads to demultiplex and I did not found any info on how to demultiplex via simpleaf, I simply created a gene2species dictionary in order to do so. My question is. if some sequences are very similar, how does simpleaf quant assign them? Does it discard them? I cannot see any qc report about reads so I am wondering.