Hello! I am annotating a plant genome with AUGUSTUS. While aligning RNASeq files to the genome with hisat2, I used a .fq file with all forward reads and another .fq file with all reverse reads. Right now, I am filtering against potentially "noisy" alignments in my sorted bam file with filterBam built in AUGUSTUS, and I used the options --uniq and --pairwiseAlignment as the reads mapped to the genome came from paired-end sequencing. The output has the following summary:
Processed alignments: 1306409009
Summary of filtered alignments:
unmapped : 542888796
percent identity: 912
coverage : 0
not unique : -452398029
singleton : 399439035
on diff. target : -575960326
Can someone tell me if the results are OK?
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