GATK-Pathseq validation

Hello,

I am using GATK Pathseq to detect bacterial sequences in rna seq mosue smaples.

The line I am using is the following

gatk --java-options "-Xms750g -Xmx750g" PathSeqPipelineSpark \
    --input sample.bam \
    --filter-bwa-image mm10_genome.fa.img \
    --kmer-file mm10_reference.bfi \
    --min-clipped-read-length 60 \
    --microbe-dict Bacteria_Sequences_removedPlasmid_Contigs_Scaffolds_Oct232015_Fusonec_Fusoval.dict \
    --microbe-bwa-image Bacteria_Sequences_removedPlasmid_Contigs_Scaffolds_Oct232015_Fusonec_Fusoval.fasta.img \
    --taxonomy-file Microbe.db \
    --output sample.pathseq.complete.bam \
    --scores-output sample.pathseq.complete_scores.csv \
    --is-host-aligned false \
    --filter-duplicates false \
    --min-score-identity .7

So I got some sequences that map to Bacillus but when I ma blasting against Bacillus I got no hits.

How could that be explained?

gatk

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updated 2.5 years ago by Ram

• written 3.5 years ago by annaA •

Hi, is your problem solved? Can you refer to this article? https://github.com/SamGa3/microbiome_reconstruction

However, I have a problem with the input bam file. The bam file obtained by star alignment of human paired-end sequencing data cannot be run after input into pathseqpipelinespark. Do you know why?

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written 2.5 years ago by nydwxsch •

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