IsoQuant Files

Secondary alignments are not used by default from now on. It significantly improves running time and RAM consumption, but barely affects the results' quality. Use --use_secondary to process secondary alignments.

New options that force IsoQuant to use only a faction of reads in high-coverage loci. Significantly improves running time and RAM consumption, but affects gene/isoform counts. New default behavior only affects small chromosomes and scaffolds (<500kbp).

In some cases, high-coverage regions take too much time to process due to extreme number of mapped reads, especially chrM (up to 10x longer compared to normal chromosomes). However, using only a fraction of these reads is enough to obtain reliable results.

These options allow to process only up to given number of reads mapping to a high-coverage loci on short and normal chromosomes:

--max_coverage_small_chr (default value is 1 million);

--max_coverage_normal_chr (default value is infinity, so usual chromosomes are not affected by default even if some genes have extreme coverage).

New option --discard_chr to discard a list chromosomes from the analysis.