STRdust BED Parsing Errors On Nanopore Data

Discovering discrepancies in how STRdust handles BED file formats can be a head-scratcher, especially when you're working with complex genomic data like Nanopore's R10 GIAB datasets. This article delves into a common issue where users encounter errors like "Chromosome chrUn_KI270376v1 is not in the fasta file or the end coordinate is out of bounds," leading them to question the BED parsing accuracy within STRdust. We'll explore the potential causes, shed light on the intricacies of BED file formats, and offer solutions to get your analysis back on track.

Understanding the "Chromosome Not Found" Error in STRdust

One of the most perplexing errors a user might encounter when running STRdust, particularly with specialized datasets like the phased R10 Nanopore GIAB data, is the "Chromosome chrUn_KI270376v1 is not in the fasta file or the end coordinate is out of bounds" message. This error, as reported by a user, typically arises when STRdust attempts to process a region defined in a BED file that doesn't seem to align with the provided FASTA reference genome. The user's FASTA file is specified as GCA_000001405.15_GRCh38_no_alt_analysis_set, and the BED file in question, GRCh38 tandem repeats BED from Sniffles, contains coordinates for tandem repeats. The immediate reaction might be to suspect an issue with the BED file itself or its compatibility with the FASTA. However, the user's troubleshooting step—running bedtools getfasta on the faulty region with the same FASTA and BED files—yielded no errors. This is a crucial piece of information, as it suggests that bedtools, a widely respected tool for genomic interval manipulation, can correctly interpret the BED file and extract the corresponding sequence from the FASTA. This strongly implies that the problem might not be with the fundamental integrity of the BED or FASTA files, but rather in how STRdust is interpreting or handling the BED file's coordinate system or formatting. The presence of chrUn prefixes in chromosome names often points to unlocalized or unassigned scaffolds within a reference genome assembly, which can sometimes be a source of parsing issues if not handled consistently across different tools.

The Nuances of BED File Format and Coordinate Systems

To truly understand the potential STRdust BED parsing issue, it's essential to have a firm grasp on the BED (Browser Extensible Data) format. While seemingly straightforward, subtle differences in how tools implement BED file parsing can lead to unexpected results. The most common point of contention, and indeed what the user rightly questions, is the end coordinate. According to the UCSC Genome Browser's FAQ, the BED format specifies that the start coordinate is inclusive, while the end coordinate is exclusive. This means that a region defined as chr1 100 200 would include bases from position 100 up to, but not including, position 200. Therefore, the total number of bases in this interval is 200 - 100 = 100. If a tool incorrectly treats the end coordinate as inclusive, it would attempt to extract 101 bases, potentially leading to out-of-bounds errors if the actual sequence ends at position 200. This is a very common pitfall when developing or using bioinformatics tools that interact with genomic intervals. Another aspect to consider is the chromosome naming convention. While human reference genomes often use prefixes like chr1, chr2, etc., some tools or specific FASTA files might omit these prefixes (e.g., 1, 2). If STRdust expects a specific convention (e.g., without chr) and the BED file or FASTA uses another, mismatches can occur, leading to the