FAQ

Does Alfred support the CRAM format?

Yes, Alfred uses HTSlib to read/write BAM/CRAM files.

Is there an example data set to test my Alfred installation?

The github source code includes a minimal example to check that alfred compiled properly from source and that the web front end is working.

alfred qc -r example/E.coli.fa.gz -o example/stats.tsv.gz example/E.coli.cram
Rscript scripts/stats.R example/stats.tsv.gz

For the web front end.

alfred qc -r example/E.coli.fa.gz -f json -o ecoli.json.gz example/E.coli.cram

Please upload ecoli.json.gz to the Alfred web application.

Is the feature counting paired-end aware?

Yes, Alfred counts fragments (read pairs) and not individual reads.

Why are hard clipping statistics always zero?

Many aligners trim primary alignments using soft-clips and only secondary and supplementary alignments use hard clips. For long reads you may want to evaluate secondary and supplementary alignments using the -s and -u command-line flags.

alfred qc -su -r <genome.fa> <input.bam>

Calculation of InDel rates and sequencing error rate?

The sequencing error rates are calculated over all aligned bases. The total number of deletions, character D in the Cigar string, is divided by the total number of aligned bases (Cigar M). The same approach is used for insertion (Cigar I) and mismatches (Cigar M and mismatch to reference).