Getting nucleotide frequencies per position
I am very new to bioinformatics and was given the task to analyze some total RNA sequencing results. So far I have converted my .fastaq files to indexed .bam using samtools index. I found the following in literature:
# Generate nucleotide counts per position samtools index -b ./sorted_bbmerge_norm_$sample.bam pysamstats -f /Users/kasenriemersma/Bioinformatics/Reference/$reference.fasta -t variation -D 1000000 --format csv --output $outputdir/ntcounts_$sample.csv ./sorted_bbmerge_norm_$sample.bam
I tried running this but I received an error that I was missing the BAM file operand. Is this there any easy way to get past this? Or is there another method that would be better?
Thanks for the help!
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