Bowtie alignment of multiple fastq files
I have 5 fastq(single-end) files from 5 replicates of wild-type samples. I want to see the read alignment percentage between each fastq file. Is there a way I can do this using bowtie or any other short read alignment alignment tools? Thank you for your help in advance.
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The Log.final.out from STAR-Align might be useful.
What exactly does between mean? If you have already done the alignments then you can use something like Qualimap (or simply
samtools stats) to generate statistics for alignments. If you usebbmap.shfor alignments then it will generate detailed alignments stats for each run by default.