User: nickhir

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nickhir20
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New User
Location:
german research cancer center (DKFZ)
Last seen:
18 hours ago
Joined:
9 months ago
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h*****************@gmail.com

Posts by nickhir

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Duplicated genes in overrepresentation analysis (ORA)
... Aright, thank you very much! I plan on comparing biopsy A vs biopsy A+biopsy B to figure out if some GO terms/pathways are significantly more mutated in biopsy A. Do you think this comparison, i.e. the choice of gene list and background makes sense? ...
written 5 days ago by nickhir20
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Comment: C: Duplicated genes in overrepresentation analysis (ORA)
... I think you missunderstood me. I know that the tool I am using removes duplicated genes. However, I am not sure if this is really the best practice for my particular type of analysis. Specifically I would like a tool that includes duplicates in its analysis. ...
written 5 days ago by nickhir20
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Duplicated genes in overrepresentation analysis (ORA)
... Hello, I have different gene lists from different biopsies. In each gene list, all genes are listed which carry a mutation (identified by WES). I want to run a overrepresentation analysis, to check if certain pathways are more hit by mutations than others. However, for many gene lists there is the ...
ora gsea written 5 days ago by nickhir20 • updated 5 days ago by kelen150
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Proper way of comparing list of mutated genes
... Hello, we performed WES on different samples, which results in a different gene lists which show which genes are mutated in the respective biopsy. I would like to compare two samples to one another and check, if for example a certain pathway/GO term carries more mutation than one might expect by ...
gene gsea written 10 days ago by nickhir20
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Comment: C: Count, LT, PH, PT Column in Functional Annotation Chart of DAVID
... Thank you for your answer! > The background is the group of all the genes in the genome. If you entered genes which are not in the genome DAVID will ignore them and they will be dropped from the list. This makes sense. But in this case I have a follow up question: What would be the best way to ...
written 11 days ago by nickhir20
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Count, LT, PH, PT Column in Functional Annotation Chart of DAVID
... Hello everybody, I am new to GSEA analysis and i use [DAVID][1] for the analysis, so please excuse if these are basic questions. I am currently analyzing WES data, and for that I compare my gene lists to different custom backgrounds. When I looked at the results of the Functional annotation chart ...
david gsea written 11 days ago by nickhir20 • updated 11 days ago by Asaf8.5k
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versioned transcripts with SnpEff GRCh37
... Hello, i have a vcf file which was generated with the GRCh37 reference genome. For downstream processing I have to annotated it with SnpEff, which works perfectly fine. The problem is that I need versioned transcripts, and with this command `java -Xmx8g -jarsnpEff.jar GRCh37.75 test.vcf > tes ...
annotation snpeff written 5 weeks ago by nickhir20
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Comment: C: GT 0/0 in VCF file
... I unfortunately do not know this. But this could be an explanation. If it was a multisample vcf file that was split, then the GT 0/0 would make sense. Thanks! ...
written 5 weeks ago by nickhir20
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GT 0/0 in VCF file
... Hello everybody, I am currently working with a one sample VCF file and a lot of my variants have 0/0 in their GT field, which means that they are homozygous for the ref base at that position if I am not mistake. If this is the case, I am wondering why they are even recorded in the VCF file in the f ...
genome written 6 weeks ago by nickhir20
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Answer: A: Extract Base Based On Position From Bam File
... I know this post is really old, but in case someone is still looking, there is a tool called [bam-readcount][1] which should do exactly what you want. Simply run ``` bam-readcount your_bam -l site_list ``` where `site_list` contains the regions of interest and has the format chr:start-stop (1 base ...
written 11 weeks ago by nickhir20

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