Open tantrev opened 7 years ago
Not sure if this is a bowtie issue or bison, but the aligned reads from bison do not seem to be properly sorted by read ID. For example, here are 20 read IDs from a file I've been aligning using bison:
SRR892990.1.1 SRR892990.2.1 SRR892990.3.1 SRR892990.4.1 SRR892990.4.2 SRR892990.5.1 SRR892990.5.2 SRR892990.1.2 SRR892990.2.2 SRR892990.3.2 SRR892990.6.1 SRR892990.6.2 SRR892990.7.1 SRR892990.7.2 SRR892990.8.1 SRR892990.9.1 SRR892990.10.1 SRR892990.11.1 SRR892990.11.2 SRR892990.12.1
Some programs like Samblaster, expect the aligned reads to be sorted so that "SRR892990.1.2" is located immediately after "SRR892990.1.1".
Not sure if this is a bowtie issue or bison, but the aligned reads from bison do not seem to be properly sorted by read ID. For example, here are 20 read IDs from a file I've been aligning using bison:
Some programs like Samblaster, expect the aligned reads to be sorted so that "SRR892990.1.2" is located immediately after "SRR892990.1.1".