Chromosome mapping with `--bed` option about alfred HOT 4 CLOSED

The mapping statistics by chromosome do not take into account a bed file. The BED file is only used for on-target and coverage per target distributions and the GC content.

from alfred.

thanks for that information. I guess we can get similar info by chromosome out of the lines that start with ^TC. however it would be nice if that were a built-in feature of alfred, because it seems that ^CM lines are not that informative when you have a target file. just a suggestion.

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additional quick question: what is the Extension metric in the OnTarget table of Alfred? i couldn't find any explanation in the alfred documentation. i see that FractionInBed matches the number given at 0 extension. could this table indicate the percent overlapping the region when it is extended left and/or right by Extension bases?

from alfred.

Exactly, alfred extends the target regions by extension bases and then re-evaluates the number of reads in a target region. That's useful because target enrichment techniques often involve capture probes and these probes might capture fragments that extend beyond the core probe (target) region.

from alfred.