Running featureCounts separately for each sample and merging results
I am running a differential expression analysis project using HISAT2 for alignment and featureCounts for assembly.
I have 27 samples with paired-end reads, and the FASTQ files alone take up about 270 GB. After running alignment for a few samples, it seems like all of the resulting BAM files after alignment with HISAT2 will likely take up well over 300 GB of space. I do not have that much storage space on my local machine, and transferring the files to Galaxy to run the analyses there will take too long.
Is it possible to run featureCounts on each BAM file separately, and then to combine the resulting raw read count matrices? Instead of running featureCounts on all of the BAM files from the alignment step at once? This way, I can align a sample of reads, run featureCounts on the BAM file, and then purge the original FASTQ and BAM files, leaving only the read count matrices which would take up much less storage space.
Any help would be much appreciated.
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