User: jrberminghamjr

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Posts by jrberminghamjr

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Mapping paired reads to reference genome, variant calling
... Thank you Jen for all of your help ...
written 12 months ago by jrberminghamjr10
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VCF filter filters everything; best forum for questions
... I have datasets that have been generated by the naive variant caller, and wish to filter them for variants that have a less than 1/10000 chance of being false positive. I used the filtering expression -f "QUAL > 40" but the output is empty. What am I doing wrong, and is this the correct approac ...
naive variant caller vcf filter questions written 13 months ago by jrberminghamjr10 • updated 13 months ago by Jennifer Hillman Jackson25k
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Mapping paired reads to reference genome, variant calling
... I am trying to map a trio of paired-end Illumina reads to a reference genome, then identify polymorphisms that are present in all three individuals; to do this, I have prepared the datasets using FASTQ groomer, and FASTQ joiner. Here are 3 questions: 1) What are the advantages/disadvantages of map ...
freebayes bowtie2 bwa naivevariantcaller written 13 months ago by jrberminghamjr10
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UCSC gene names
... I have uploaded a database of genes from the UCSC genome browser (Hg38) to Galaxy, to identify the genes with the largest number of polymorphisms in paired-end sequences from a trio (for a Coursera project). I have two questions: 1) the name column in the uploaded dataset does not have standard gen ...
ucsc genome browser gene name coursera written 13 months ago by jrberminghamjr10 • updated 13 months ago by Jennifer Hillman Jackson25k
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How does a poster delete unwanted posts?
... How does one delete duplicate posts, and/or posts based on mistaken information that the poster does not wish others to waste their time reading? Thanks ...
posts written 13 months ago by jrberminghamjr10 • updated 13 months ago by Jennifer Hillman Jackson25k
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Bowtie2 Select Reference Genome; eliminating false positive variants
... Three questions: 1) When specifying a reference genome, what are the advantages and disadvantages of using Hs38 vs Hs38 canonical? 2) On Bowtie2, under "select reference genome", my workflow says Hs38 (Homo sapiens), but cuts off before I can determine if it is set ot Hs38 or Hs38 canonical. Clicki ...
bowtie2 vcf reference genome written 13 months ago by jrberminghamjr10
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get data, data limits
... 3 quick questions: 1) I want to start a new workflow, and I have datasets downloaded. However, when I use "Get Data" the option of accessing those datasets is not highlighted; what am I doing wrong? 2) My datasets together are ~110GB, and I understand that the public galaxy has a data limit (25 ...
galaxy written 13 months ago by jrberminghamjr10 • updated 13 months ago by Martin Čech ♦♦ 4.8k
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Galaxy 101: UCSC browser User Supplied Track missing item
... I am following the Galaxy 101 tutorial, and have placed the top polymorphisms on the UCSC browser successfully. However, the tutorial has an option to "Show only items with score at or above ", in which it appears that the user can enter a value into the box. This line is missing in the UCSC wind ...
ucsc browser galaxy written 14 months ago by jrberminghamjr10 • updated 14 months ago by Jennifer Hillman Jackson25k
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Comment: C: Galaxy101: downloading Chr22 exon data
... Thanks; I've managed to proceed, but now I've discovered that the UCSC browser doesn't show the custom track that I should have generated.... John ...
written 14 months ago by jrberminghamjr10
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Galaxy101: downloading Chr22 exon data
... Additional problem from last post: Traceback (most recent call last): File "/galaxy-repl/main/jobdir/016/289/16289368/set_metadata_AijlGT.py", line 1, in from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/cvmfs/main.galaxyproject.org/galaxy/l Is this due to a slow co ...
software error written 14 months ago by jrberminghamjr10 • updated 14 months ago by Jennifer Hillman Jackson25k

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