User: bryantl

gravatar for bryantl
bryantl90
Reputation:
90
Status:
Trusted
Location:
United States
Last seen:
1 year, 1 month ago
Joined:
2 years, 7 months ago
Email:
b******@mail.med.upenn.edu

Posts by bryantl

<prev • 20 results • page 1 of 2 • next >
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Viewing BAM files on UCSC genome browser
... I typically view BAM files on the UCSC genome browser to double check coverage of genes that I am particularly interested in. I noticed today that the option has disappeared and the files that I had already loaded as custom tracks in UCSC genome browser are no longer able to be viewed. Does anyone ...
bam written 16 months ago by bryantl90 • updated 16 months ago by Jennifer Hillman Jackson25k
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Comment: C: fastq.gz file can not auto uncompress
... I am having the same problem. Does anyone know if there is a way to unzip the file in Galaxy if it fails to do so automatically? ...
written 17 months ago by bryantl90
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Comment: C: Public Galaxy stuck
... Thanks! It does seem to be working now. The jobs that were already running when the delay started actually did fail. Once it started working again I was able to rerun those jobs without problem. ...
written 22 months ago by bryantl90
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Comment: C: Public Galaxy stuck
... I'm having the same problem. Jobs stopped running on Saturday for me. ...
written 22 months ago by bryantl90
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Jobs waiting to run
... I have had jobs waiting to run since yesterday. Is Galaxy slow in general right now or should I delete them and retry? ...
galaxy written 22 months ago by bryantl90 • updated 22 months ago by Nate Coraor3.2k
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Answer: A: Multiple fastq files in Bowtie2
... You could concatenate the datasets so that you are inputing one fastq file for R1 and one file for R2. ...
written 22 months ago by bryantl90
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Comment: C: can't get any VCF tools to work
... I think the tools are having problems today. I haven't been able to get any jobs to run correctly. ...
written 23 months ago by bryantl90
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Answer: A: fastq to bam
... Try using Fastq Groomer on your fastq files before mapping. This will ensure that your files are in the correct format. Assigning the quality encoding scheme if you do not know it is correct does result in errors. For the next steps you might find this helpful: https://wiki.galaxyproject.org/Le ...
written 23 months ago by bryantl90
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Coverage for specific genes and exons
... I am using a whole exome sequencing dataset to look for potential pathogenic mutations. Overall, I have good coverage, but some regions of interest do not have good coverage and generate a false negative result. Is there a way to check coverage in a list of genes using galaxy to know if any have p ...
bam galaxy written 23 months ago by bryantl90 • updated 23 months ago by Jennifer Hillman Jackson25k
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Answer: A: Problem with bam files for exome sequencing analysis
... From your answers it looks like you do not have a database set for your BAM file. In order for any of the tools to process your data, you will have to indicate which build was used to make it. You can check whether or not the build is indicated on your file in galaxy by clicking on the file in you ...
written 23 months ago by bryantl90

Latest awards to bryantl

Scholar 2.1 years ago, created an answer that has been accepted. For A: To varscan mpileup data
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: To varscan mpileup data

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