User: j.lunger18

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j.lunger1810
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Posts by j.lunger18

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Comment: C: MD5 not the same between contig and reference; both Unified Genotyper and Haplot
... Thanks, I downloaded the reference file from TCGA. Should I be concerned that the MD5 from this file doesn't match either of the MD5s that were in my error? From your link: GRCh38.d1.vd1.fa.tar.gz md5: 3ffbcfe2d05d43206f57f81ebb251dc9 From my error: contig reads: 6c198acf68b5af7b9d676dfdd531b5d ...
written 10 hours ago by j.lunger1810
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MD5 not the same between contig and reference; both Unified Genotyper and Haplotype Caller
... I'm trying to call variants for a large number of bam files, but continue to get the following error: ##### ERROR contig reads is named chr9 with length 138394717 and MD5 6c198acf68b5af7b9d676dfdd531b5de #### ERROR contig reference is named chr9 with length 138394717 and MD5 addd2795 ...
vcf gatk md5 written 11 hours ago by j.lunger1810 • updated 11 hours ago by igor9.9k
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Comment: C: R Package for Visualizing SNVs from "sites only" VCF (population variants)
... Ideally something that can load in ensembl transcript and protein domain information for a gene of interest ...
written 16 hours ago by j.lunger1810
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Comment: C: R Package for Visualizing SNVs from "sites only" VCF (population variants)
... I already annotated the files. I want a tool that can take all that information associated with each variant and visualize it in a way that is more digestible than a huge dataframe aka a mutation lollipop chart, multiplexed graphs, etc. ...
written 16 hours ago by j.lunger1810
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Comment: C: R Package for Visualizing SNVs from "sites only" VCF (population variants)
... Considering this type of file is what gnomAD variants are formatted in, I figured there may be tools to visualize annotated versions of these files. ...
written 1 day ago by j.lunger1810
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Comment: C: R Package for Visualizing SNVs from "sites only" VCF (population variants)
... Population "sites only" VCFs can still be annotated, so I have a lot of information on predicted impact of each variant on protein function, frequency in different populations, etc. I have a lot of information on each variant, but no sample-specific information. ...
written 1 day ago by j.lunger1810
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R Package for Visualizing SNVs from "sites only" VCF (population variants)
... I found GenVisR, which has a nice variant visualization tool (Lollipop), but the VCF I have is downloaded from gnomAD, so does not have individual sample information. Is there another tool that can be used to visualize this kind of data? ...
snvs R vcf written 3 days ago by j.lunger1810
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Comment: C: GENCODE and untranslated regions
... Great, thank yoU! ...
written 3 months ago by j.lunger1810
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GENCODE and untranslated regions
... I want to pull variants from a specific gene and for that I need chromosomal locations. I'm using the UCSC browser to get a range of positions for my gene. I want to include untranslated regions that flank the transcript. I found that the GENCODE transcripts are easy to click on to find their chromo ...
utr gencode written 3 months ago by j.lunger1810 • updated 3 months ago by Emily_Ensembl20k
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Extracting VCF of all variants in TCGA exomes from all cancer types
... Hi. Ideally, I would like to get a single VCF file from all the exomes sequences that TCGA has from all cancer types. Even more ideally, I would do this for only a certain region in the genome. Is there any way to do this? I have GDC-client downloaded and loaded in the command line at the moment, bu ...
vcf tcga written 4 months ago by j.lunger1810 • updated 4 months ago by Kevin Blighe56k

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