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I am trying to generate bam files from reads (originally in fasta format) with ‘artifical Q-score’ generated with the attached script ‘fasta_to_fastq’
First step : I created fastq file from source fasta file (R1R2.fasta attached)
Second step: I am trying to convert the R1R2.fastq file to bam file (here I am using FastqToSam command below)
Final step (my goal): use the bam file as input for haploclique (https://github.com/cbg-ethz/haploclique)
java -jar /Users/antoinechaillon/Documents/HIV/TOOLS/picard-tools-1.89/picard-tools-1.89/FastqToSam.jar F1=R1R2.fastq O=R1R2.bam SM=for_tool_testing
I get this error (screenshot)
thoughts? alternative approach?
thanks for your help ++