I noticed that qtip stores any alignments as SAM. This can be huge and therefore very problematic with real data. Could you please consider storing BAM instead? The overhead of compression and decompression on the fly should be negligible. Moreover, it will be even faster to read and write a BAM on most systems, because much less has to be written to disk.
I noticed that qtip stores any alignments as SAM. This can be huge and therefore very problematic with real data. Could you please consider storing BAM instead? The overhead of compression and decompression on the fly should be negligible. Moreover, it will be even faster to read and write a BAM on most systems, because much less has to be written to disk.