"Missing flanking read fragments"

[hchetia]

Hi Egor @egor-dolzhenko

I am using a bam file with manually selected paired end reads aligned with Repeat Unit (genomic location used as defined in the variant catalog) to generate a reviewer plot. We extracted these reads from the realigned bam file generated by Expansion Hunter.

I get the foll. error-

"Missing flanking read fragments"

What would this error message imply and is there a way to rectify this?

[egor-dolzhenko]

Hi Hasna,

Thanks for the question. REViewer estimates the fragment length from read pairs that align within the sequence surrounding the repeat. Are you extracting reads from the realigned BAM file because you want to highlight specific alignments?

Best wishes,
Egor

[hchetia]

Hi Egor,
"Are you extracting reads from the realigned BAM file because you want to highlight specific alignments?"

-Yes. My actual aim is to find a way to estimate mismatches or gaps in the alignment within the repeat region. The CIGAR string in the realigned file is helpful but it is not specific for the repeat region only.