filterBam (Augustus) results explanation
Entering edit mode
3 months ago
Sanam • 0

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?

GenomeAnnotation RNASeq Annotation filterBam Augustus • 229 views

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