Use you results from exercise 3, where you split data according to barcodes and then trimmed them (cleaned out of technical sequences, adaptors and barcodes). Here you have sequence of HIV1. Use programs bwa and bowtie2 and map sample1 to the HIV sequence, use both original data and your trimmed data.
Compare number of mapped sequences in bwa and bowtie2 mapping. Check few reads and compare, if your trimming was ok or if you left some technical sequences as part of the read.
Use samtools and get id of all unmapped reads (flag 4), sort the output and index final bam file.
Visualize results using tablet and/or
IGV.
Here are some hints (these are not copy/paste commands, just a hints):
bwa index -p HIV1 HIV1.fna
bwa mem -t 2 HIV1 ex3_smpl1.fastq >ex3_smpl1-bwa.sam
bowtie2-build HIV1.fna HIV1
bowtie2 -p 2 -x HIV1 -U ex3_smpl1.fastq >ex3_smpl1-bowtie2.sam
samtools flagstat
samtools view -F 4
samtools sort
samtools index
Here is the HIV1 sequence and my results for your controll.
Time-stamp: <2022-11-09 12:36:04 (hpaces)>