Open MicSonn opened 5 years ago
Dear All, I'm a bioinformatics. I have read your QTip paper. I'm interested in trying QTIP on my NGS data. When I apply qtip with Bowtie2 it's OK, but with bwa it does not work.
Similarly to Boutie2: Bwa index ../AiV1GenRef.fasta IndexBWA/AiV1GenRef BWA_ARGS="-I 3L,L/4" qtip \ --ref ../AiV1GenRef.fasta \ --m1 ../R1.trim.fastq.gz --m2 ../R2.trim.fastq.gz \ --index IndexBWA/AiV1GenRef --bwa-exe path/bwa \ --keep-intermediates \ --temp-directory Out/ --output-directory QTip1/ --write-orig-mapq --write-precise-mapq -- ${BWA_ARGS}
I’ve installed QTip with Bioconda (conda install qtip).
Is there a procedure that I may have to do after installation with conda? Can you help me understand where the problem is?
Thank you very much, Michele Sonnessa
Dear All, I'm a bioinformatics. I have read your QTip paper. I'm interested in trying QTIP on my NGS data. When I apply qtip with Bowtie2 it's OK, but with bwa it does not work.
Similarly to Boutie2: Bwa index ../AiV1GenRef.fasta IndexBWA/AiV1GenRef BWA_ARGS="-I 3L,L/4" qtip \ --ref ../AiV1GenRef.fasta \ --m1 ../R1.trim.fastq.gz --m2 ../R2.trim.fastq.gz \ --index IndexBWA/AiV1GenRef --bwa-exe path/bwa \ --keep-intermediates \ --temp-directory Out/ --output-directory QTip1/ --write-orig-mapq --write-precise-mapq -- ${BWA_ARGS}
I’ve installed QTip with Bioconda (conda install qtip).
Is there a procedure that I may have to do after installation with conda? Can you help me understand where the problem is?
Thank you very much, Michele Sonnessa