User: garzetti

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garzetti100
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100
Status:
New User
Location:
Germany
Last seen:
4 years ago
Joined:
4 years, 9 months ago
Email:
g*******@mvp.uni-muenchen.de

Posts by garzetti

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Variant Annotation In Galaxy
... Hello, is there a tool in the main Galaxy to extract a fasta alignment of my detected variants from a vcf file? I have 19 samples (plus the reference). Thanks! Debora ...
written 4.4 years ago by garzetti100
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Comment: C: Variant Annotation In Galaxy
... Hi Jen, thanks for your answer! Unfortunatelly I cannot run Galaxy locally (in my Institute we only have Windows computers), but I can try on a cloud. I have a DIAG account, do you know if Galaxy works there? Debora ...
written 4.4 years ago by garzetti100
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Variant Annotation In Galaxy
... Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genomes and look which of them cause non-synonymous mutations. I have found two tools in the Main Galaxy that I can use for this purpose (snpEff and Annovar), but I have problems with them. How can I change t ...
snp snpeff written 4.4 years ago by garzetti100 • updated 4.4 years ago by Jennifer Hillman Jackson25k
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Read Simulator
... Dear all, I would like to perforn my SNP calling pipeline (for MySeq Illumina reads) to previously sequenced and assembled genomes. Is there any read simulator in the Main Galaxy? I am looking for something like the wgsim algorithm in SAMtools... Thanks! Debora ...
bam samtools written 4.4 years ago by garzetti100 • updated 4.4 years ago by Xianrong Wong90
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Workflow Does Not Run
... Hello! I have a question about a workflow I have created from my history. I can edit and view it, but when I try to run it, a white page appears and I cannot do anything. I have created other worflows which perfectly run, but I don't know why this one doesn't. It includes 4 steps for GATK pre-proce ...
gatk written 4.6 years ago by garzetti100 • updated 4.6 years ago by Jennifer Hillman Jackson25k
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Problems With Picard And Gatk Tools
... Dear all, I have been trying to analyze some recently acquired WGS reads (re-sequencing with MiSeq) but I am having problems with both Picard and GATK tools and I don't know where the problem is. My fastq reads are already in the sanger/illumina 1.9 format, as recognized by the FastQC tool. I have ...
alignment bwa written 4.6 years ago by garzetti100
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Re: Snp Calling Problems (Jennifer Jackson)
... Hi Jen, thank you for your answer! I have used the Add or Replace group tool and it worked pretty well, so that I could use the FreeBayes tool with no problem! Now I have another question: I have been pre-processing my data with the NGS: GATK tools according to their Best Practices and I am ready ...
galaxy written 4.8 years ago by garzetti100 • updated 4.8 years ago by Jennifer Hillman Jackson25k
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Main Galaxy Server Is Down?
... I have the same problem with the BWA mapping tool (jobs waiting for run since Friday), but other tools (e.g. SAMtools) are working. My analysis also depends a lot on these mapping data! Debora -- Debora Garzetti, PhD Student AG Rakin Max von Pettenkofer-Institute, LMU Pettenkoferstraße 9A 80336 Mu ...
bam samtools alignment bwa written 4.8 years ago by garzetti100 • updated 4.8 years ago by Jennifer Hillman Jackson25k
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Snp Calling Problems
... Dear all, I have been looking for an answer to my problem in all the Galaxy Support resources but with no success. I am sorry if this topic has been already discussed! So, I am analyzing MiSeq data on the main Galaxy. I have Fastq files from 4 paired-end samples. After having checked the quality w ...
bam samtools alignment bwa written 4.8 years ago by garzetti100 • updated 4.8 years ago by Jennifer Hillman Jackson25k

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