I am a newbie in these bioinformatics tools. I have 42 x 2 (paired end) fastq files that got from Illumina Miseq run for Gallus gallus DNA.
I need to convert them into bam files to analyze. I tried to use FastqtoSam converter (gives unaligned bam files) under NGS:Picard for two files for trying but I couldn't do it. Firstly, I selected Illumina (+64) as quality encoding scheme but it gave error. Then I chose Sanger (+33) and it gave bam files which is not opened with IGV (Integrative Genomics Viewer). IGV gives error "An index file is required for SAM&BAM files". I think I did something wrong.
Could you lead me about converting fastq files into bam. Please explain step by step.
Thank you in advance.