Hello,

I hope this is the right forum for my question or that someone can help at all. I'm somewhat new to analyzing NGS data in general, but I am trying to analyze some published ribo-seq data. I have aligned it myself and trimmed the reads by quality. When I view these alignments in IGV, for example, I can see that the reads cover a reference span that makes sense for ribo-seq data (between 25 and about 34 bp), but when I load this same BAM file into the readRibodata() function it produces read widths of only 50bp (presumably the pre-trimmed read length). I am unsure if I have done something wrong in my alignment procedure (done with bowtie2), or if there is a way to have readRibodata() utilize the CIGAR string or some other info from the BAM file. Any help is appreciated.

Here is what the code shows:

riboDat <- readRibodata('Ribobt2local1milsort.bam', replicates = 'LB') Reading ribosomal files....done! table(width(riboDat@riboGR$Ribobt2local1milsort.bam))

50

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