Subread and featurecounts read index and annotation once for all

Question

[bharata1803]

Hello,

I noticed that subread aligner and featurecounts software both loading the index and annotation at the beginning. If I want to process multiple fastq and bam, is it possible to process it at once? Loading the index itself take several minutes so if there are any methods to bulk align and bulk read counts, it would save time quote a lot.

[WouterDeCoster]

Not what you are asking for, but if saving time is what you want (and you have a well-annotated organism) you could take a look at pseudoalignment using salmon or kallisto.

[bharata1803]

Usually I use salmon, but this time the fastq is colorspace. So, I need to use aligner that support colorspace which is subread. I am used to use salmon with fast process and now stuck in subread with 30 minutes per file processing.