# FAQ
For questions, help or feature requests please contact gear_genomics@embl.de
# 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).