User: a.james

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a.james210
Reputation:
210
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Location:
Switzerland
Last seen:
an hour ago
Joined:
6 years, 7 months ago
Email:
a******@dkfz-heidelberg.de

Posts by a.james

<prev • 106 results • page 1 of 11 • next >
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Comment: C: List of TCGA genes differentially expressed in normal versus tumor
... there is no option to download the differentially expressed genes ...
written 4 weeks ago by a.james210
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How to get the refSNP ids or rsIDs of variants from UKbiobank datasets
... Dear All, I have a list of variants from UKbiobank pipelines. Now, I need to annotate them with GWAS catalog, for that, I need the refSNP id or rsids. The current variants have no rsiDS for them. I would like to extract that, could someone please suggest something for that? I have seen Biomart, an ...
genome next-gen snp sequencing written 6 months ago by a.james210
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Comment: C: Download the promoter, enchancer, TSS , 3 prime, exon and intron positions of al
... Thank you for the detailed reply. I will take a look :) ...
written 7 months ago by a.james210
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Download the promoter, enchancer, TSS , 3 prime, exon and intron positions of all hg38 genes
... Hi All, I would like to download the promoter enhancer, exon, intron, 3'prime, 5'prime positions of all genes from the human genome hg38 version. I have seen a couple of information in the ENSEMBLE and FANTOM website, however, the above-mentioned information is not able to find out. For example, ...
dna-seq rna-seq written 7 months ago by a.james210 • updated 7 months ago by Shalu Jhanwar490
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how to extact first 100 lines of an indexed BED file
... I would like to know is there a way to extract lines of an indexed `BED` file, when you do not have the original BED file. I have an indexed bed file, from which I would like to subset it to a toy bed file for testing a script. Any suggestions are greatly appreciated!! ...
genome bed written 10 months ago by a.james210
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How to annotate illumina HumanHT-12_V3_0_R3_11283641_A.txt data
... Dear All, I have Illumina array probe metadata with me `HumanHT-12_V3_0_R3_11283641_A.txt`. Now, I need to annotate the gene symbols present within them. Precisely, I need to know the biotype of all genes available in the Illumina metadata file. The file consists of 48k genes. When I use GENCODE `G ...
genome illumina array written 10 months ago by a.james210
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Comment: C: Tools for predicting the protein altering effects of the variants from EXON-seq
... @Pierre Thanks for the link! That's helpful. ...
written 12 months ago by a.james210
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Tools for predicting the protein altering effects of the variants from EXON-seq data
... Hi Say I have a lot of variants including INDELS, SNVs, SNPs, etc from the exon-seq dataset. Now, I need to predict whether or not they have any protein-altering effects (for eg. missense, sense), etc.. I need to know whether or not there are any tools available for this which I can use on the comm ...
variants exon-seq snp sequencing written 12 months ago by a.james210
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Finding the coverage of variants from variant file, which has no DF4 field
... Hello All, I have a simulated VCF file and I have simulated fastq file generated using the `varsim` tool. I wanna find the coverage of each variants in the `vcf` file. The `vcf` file has no filed (for example, DF4 field with coverage information). Inorder to find the coverage I first aligned the fa ...
assembly rna-seq written 15 months ago by a.james210
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Comment: C: The Picard FilterSAM READ is throwing error
... Thanks for the reply. It was previously sorted on the read_id using `samtools sort -n`. ...
written 15 months ago by a.james210

Latest awards to a.james

Popular Question 5 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 5 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Centurion 10 months ago, created 100 posts.
Popular Question 10 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 15 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 19 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 19 months ago, created a question with more than 1,000 views. For Healthy donor RNA-seq samples
Scholar 22 months ago, created an answer that has been accepted. For A: GeneSCF gives out more pathways for genes compared to DAVID
Popular Question 22 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 23 months ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 2.1 years ago, created a question with more than 1,000 views. For BED file with amplicon information
Popular Question 2.9 years ago, created a question with more than 1,000 views. For GeneSCF gives out more pathways for genes compared to DAVID
Popular Question 2.9 years ago, created a question with more than 1,000 views. For BED file with amplicon information
Great Question 3.0 years ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 3.2 years ago, created a question with more than 1,000 views. For BED file with amplicon information
Great Question 3.7 years ago, created a question with more than 5,000 views. For ALL RNA-seq publicly available data
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How to find the frame shift information from fusion gene sequence
Popular Question 3.7 years ago, created a question with more than 1,000 views. For DESeq output from RNA-seq
Popular Question 4.2 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Student 4.5 years ago, asked a question with at least 3 up-votes. For ALL RNA-seq publicly available data
Popular Question 4.5 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Popular Question 4.6 years ago, created a question with more than 1,000 views. For ALL RNA-seq publicly available data
Scholar 4.6 years ago, created an answer that has been accepted. For A: GeneSCF gives out more pathways for genes compared to DAVID
Supporter 4.6 years ago, voted at least 25 times.
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Pathway Graphs for gene set from RNA-seq

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