User: a.james
a.james • 210
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Posts by a.james
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... there is no option to download the differentially expressed genes ...
written 4 weeks ago by
a.james • 210
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... 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 ...
written 6 months ago by
a.james • 210
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... Thank you for the detailed reply. I will take a look :)
...
written 7 months ago by
a.james • 210
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... 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, ...
written 7 months ago by
a.james • 210
• updated
7 months ago by
Shalu Jhanwar • 490
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... 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!!
...
written 10 months ago by
a.james • 210
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... 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 ...
written 10 months ago by
a.james • 210
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... @Pierre Thanks for the link! That's helpful.
...
written 12 months ago by
a.james • 210
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... 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 ...
written 12 months ago by
a.james • 210
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... 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 ...
written 15 months ago by
a.james • 210
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... Thanks for the reply. It was previously sorted on the read_id using `samtools sort -n`. ...
written 15 months ago by
a.james • 210
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