Base editors convert one base into another at a target site without cutting both strands, so the question they raise is not "how big was the indel" but "which base changed, where, and how often". BE-Analyzer answers that from the sequencing reads of an edited amplicon: it merges paired reads, aligns each distinct read against the reference, and reports the conversion rate at every position, the breakdown of what each edited base became, and the alleles behind those numbers.
Required. Paired reads are merged with a fastq-join port before alignment.
Optional, from an untreated sample. With one, the charts mirror its substitution rate below zero, so background reads as background.
The protospacer only, without the PAM. It has to appear in the reference on one strand or the other.
Positions counted upstream of the PAM. Conversions of C to T inside this window are what the editing rate counts.
How far either side of the protospacer the table and charts reach.
Sequences seen n times or fewer are discarded before analysis.
A folder of FASTQ files. Reads are paired by filename — _R1/_R2,
including the full Sample_S1_L001_R1_001.fastq.gz form, or a trailing
_1/_2.
Every sample uses the form below unless a manifest overrides it.
CSV or TSV overriding the form per sample. Only sample is required;
recognised columns are r1, r2, fullseq,
rgenseq, addval, nval, lrval,
startwin, endwin, before,
after, rev and control.
This browser has no origin-private file system, or the page is not in a secure context, so alignments cannot be stored. Everything else works.
The protospacer only, without the PAM. It has to appear in the reference on one strand or the other.
Positions counted upstream of the PAM. Conversions of C to T inside this window are what the editing rate counts.
How far either side of the protospacer the table and charts reach.
Sequences seen n times or fewer are discarded before analysis.