User: BC357

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BC35770
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United States
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2 years, 3 months ago
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3 years ago
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b***********@mssm.edu

Posts by BC357

<prev • 25 results • page 1 of 3 • next >
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Comment: C: cuffmerge encounters errors in gtf/gff files
... Thank you very much for the suggestion. I will try to upload another GFF3 ref genome/annotation to run my cufflinks .gtf output against and see if the error would be gone. If not, I will try to remap my initial BAM to a new ref genome. Apology for my poorly worded question, as I am not well versed ...
written 2.3 years ago by BC35770
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cuffmerge encounters errors in gtf/gff files
... Does anyone know how to fix the following cuffmerge errors? Initially I thought it's the "reference annotation" file that was not recognized (as I have gff in the history : GCF_000001635.24_GRCm38.p4_genomic.gff). However, when I wanted to switch the reference file to GTF ( Mus_musculus.GRCm38.81.g ...
cufflinks cuffmerge written 2.3 years ago by BC35770 • updated 2.3 years ago by Jennifer Hillman Jackson23k
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Answer: A: ANNOVAR annotate cuts short the VCF file ?
... Sorry for missing your feedback. Indeed, I was using the tool on the public Main Galaxy and did notice the warning of ANNOVAR no longer does line-to-line conversion. From your response, it sounds like the team is reviewing an update to address the issue of ANNOVAR. If correct, is there any fix/solut ...
written 2.9 years ago by BC35770
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Comment: C: ANNOVAR annotate cuts short the VCF file ?
... comment cancelled and re-posted as an answer. ...
written 2.9 years ago by BC35770
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SnpEff supports only genomes of two species?
... Under usegalaxy, I was trying to use SnpEff to annotate my VCF, but the genome dropdown list shows only the genomes from C. elegans and Brachypodium, No genome of any version for homo sapiens ?? Is there no way to include human genomes in SnpEff on the main page? ...
snpeff written 2.9 years ago by BC35770 • updated 2.9 years ago by Jennifer Hillman Jackson23k
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ANNOVAR annotate cuts short the VCF file ?
... I uploaded a standard VCF that contains 57651 lines (or 57471 lines variant data) and ran it with ANNOVAR , under usegalaxy.org, to annotate the variants. To my surprise, the output from ANNOVAR contains only 24072 variants. When I aligned the two tables, it's clear ANNOVAR "removed" some of the var ...
annovar written 2.9 years ago by BC35770
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questions about read groups
... As my prior question didn't seem to get a response, which was wrapped in my OP as a comment, I am re-posting it as a new question, hoping to get some feedback. It seems that GATK tools require all files/input to be "read groups verified". However, I just realized the "commonly used setting" of BWA ...
read groups written 3.0 years ago by BC35770 • updated 3.0 years ago by Jennifer Hillman Jackson23k
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Comment: C: any plan to provide other variant caller tools ?
... Thank you very much for the update! Will take a look at Freebayes and Naive Variant Caller. In my limited experience, using Tool Shed in a local or cloud Galaxy requires more resources and computer know-how. usegalaxy.org on the other hand has an easy interface that allows non-bioinformaticians to g ...
written 3.0 years ago by BC35770
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Comment: C: any plan to provide other variant caller tools ?
... I meant usegalaxy.org  ...
written 3.0 years ago by BC35770
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any plan to provide other variant caller tools ?
... From what I could find, Galaxy currently provides Varscan and UnifiedGenotyper for variant calling. It appears that there are other tools available and some seem to outperform Varscan and UnifiedGenotyper. For example, GATK's Haplotypecaller is recommended over UnifiedGenotyper, although it does see ...
variant caller written 3.0 years ago by BC35770 • updated 3.0 years ago by Jennifer Hillman Jackson23k

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