User: Sebastian Boegel

Reputation:
480
Status:
Trusted
Location:
Germany
Twitter:
sebboeg
Scholar ID:
Google Scholar Page
Last seen:
2 days, 17 hours ago
Joined:
7 years, 4 months ago
Email:
s*********@googlemail.com

Bioinformatician and PhD student in cancer research

Posts by Sebastian Boegel

<prev • 31 results • page 1 of 4 • next >
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whole blood RNA-seq without globin depletion
... I was asked to analyze whole blood RNA-Seq data and realized huge amounts of HBA1,2, HBB transcripts. So obviously the wet lab team has not done globin depletion. I would love to advice them for the next experiments, to do globing depletion, however I realized that all the public available SRA data ...
hemoglobin rna-seq written 2 days ago by Sebastian Boegel480 • updated 2 days ago by h.mon29k
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Comment: C: Using single sample gsea with tpm file
... Thank you very much Igor for your helpful reply. One more question: are you aware of a step by step walkthrough or example code how to (correctly) perform gene set enrichment analysis with one sample (table of genes and 1 column with gene expression values (in tpm))? Thanks again for your help, S ...
written 2 days ago by Sebastian Boegel480
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Using single sample gsea with tpm file
... I have a single RNA-Seq sample analyzed with kallisto and the output is a tsp with 170k lines (transcripts) and tpm values. I want to do single sample pathway enrichment (gene set enrichment), but I am not sure what, how to further preprocess the Kallisto output to fit into gsva, esp.: 1.) I need E ...
ssgsea kallisto gene set enrichment rna-seq written 6 days ago by Sebastian Boegel480 • updated 6 days ago by igor8.9k
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Comment: C: Querying raw TCGA sequencing data on GDC
... Thanks for your help. This was exactly what i was looking for. ...
written 3.4 years ago by Sebastian Boegel480
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Querying raw TCGA sequencing data on GDC
... I realized that TCGA Data Access moved from cghub to GDC. Before the move i was using cquery and gtdownload to search and download TCGA raw sequencing data (we have dbgapo permission). Especially the search tool was great as it allows to search e.g.: Show me all BRCA RNA-Seq samples in fastq (i.e. n ...
tcga gdc rna-seq written 3.4 years ago by Sebastian Boegel480
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Answer: A: 1000 genomes data fastq
... This is all exome-seq, right? No, RNA-Seq available? ...
written 4.7 years ago by Sebastian Boegel480
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Answer: A: Has the RNA-Seq Atlas website closed?
... Dear Russ, that is odd. The page doesnt load anymore. Maybe you contact the first author, mail adress can be found at http://www.ncbi.nlm.nih.gov/pubmed/22345621 In the meantime you can try the TRON Expression Atlas. It is new (manuscript submitted) and consists of public RNA-Seq data processed in ...
written 4.7 years ago by Sebastian Boegel480
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Answer: A: Healthy donor RNA-seq samples
... The GTEX project is what you looking for (http://www.gtexportal.org/home/) For accessing the raw data (fastqs) you need to apply. ...
written 4.7 years ago by Sebastian Boegel480
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Answer: A: Rna-Sequencing For Nci-60 Data
... The Cell Reports paper mentioned above uses Microarray gene expression data. I am also searching for NCI60 RNA-Seq data. cghub was mentioned in an answer above. In case of mean: https://cghub.ucsc.edu/datasets/data_sets.html, there is unfortunately no NCI60 RNA-Seq dataset to download. Or is the NC ...
written 4.8 years ago by Sebastian Boegel480
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Answer: A: CCLE RNA-seq library protocol
... Hi, just stumbled over your post. I dont know, if that still helps: "Large insert non-strand specific RNA Sequencing included plating, poly-A selection and cDNA synthesis, library preparation (400bp insert), sequencing (101bp paired reads) and a sample identification QC check. Non-strand specific ...
written 4.9 years ago by Sebastian Boegel480

Latest awards to Sebastian Boegel

Appreciated 3.4 years ago, created a post with more than 5 votes. For A: How to download a full matrix of gene expression of a TCGA dataset
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Querying raw TCGA sequencing data on GDC
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Find Her2 copy number by FISH in TCGA BRCA clinical file
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Has the RNA-Seq Atlas website closed?
Appreciated 4.6 years ago, created a post with more than 5 votes. For A: How to convert to .SRA files to .FQ (FASTQ)
Appreciated 4.6 years ago, created a post with more than 5 votes. For A: How to download a full matrix of gene expression of a TCGA dataset
Good Answer 4.6 years ago, created an answer that was upvoted at least 5 times. For A: How to convert to .SRA files to .FQ (FASTQ)
Good Answer 4.6 years ago, created an answer that was upvoted at least 5 times. For A: Software For Hla Typing Using Ngs?
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Question about Somatic and Germline with homozygous and heterozygous
Scholar 4.7 years ago, created an answer that has been accepted. For A: How to download a full matrix of gene expression of a TCGA dataset
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Question about Somatic and Germline with homozygous and heterozygous
Scholar 4.7 years ago, created an answer that has been accepted. For A: How to download a full matrix of gene expression of a TCGA dataset
Scholar 4.9 years ago, created an answer that has been accepted. For A: How to download a full matrix of gene expression of a TCGA dataset
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Question about Somatic and Germline with homozygous and heterozygous
Appreciated 5.3 years ago, created a post with more than 5 votes. For A: How to convert to .SRA files to .FQ (FASTQ)
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Question about Somatic and Germline with homozygous and heterozygous
Scholar 5.4 years ago, created an answer that has been accepted. For A: How to download a full matrix of gene expression of a TCGA dataset
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Question about Somatic and Germline with homozygous and heterozygous
Scholar 5.4 years ago, created an answer that has been accepted. For A: How to download a full matrix of gene expression of a TCGA dataset
Scholar 5.5 years ago, created an answer that has been accepted. For A: How to download a full matrix of gene expression of a TCGA dataset

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