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1
vote
3
replies
560
views
differential gene expression gene names/id vs transcript id
volcano-plot
updated 10 months ago by 82k • written 10 months ago by ▴ 80
3
votes
3
replies
547
views
DESeq2: "model matrix is not full rank"
deseq2
updated 10 months ago by 10k • written 10 months ago by ▴ 80
0
votes
0
replies
317
views
extracting gencode 3utr and 5utr as part of R pipeline
5utr 3utr
12 months ago by Jalil Sharif ▴ 80
0
votes
9
replies
1.5k
views
Intersecting transcriptome bam file with GTF file
findoverlaps bedtools transcriptome
updated 12 months ago by ▴ 900 • written 12 months ago by ▴ 80
0
votes
6
replies
1.2k
views
samtools and Rsamtools in r
samtools
updated 10 months ago by 43k • written 12 months ago by ▴ 80
6
votes
7
replies
1.0k
views
extracting data from single end aligned bam file - chromosome, strand, start and stop from cigar
bam
updated 12 months ago by 100k • written 12 months ago by ▴ 80
2
votes
4
replies
871
views
Artificial reads - remove multiple mapped reads against reference genome, and only keep reads that completely match without any mismatches - samtools
samtools
13 months ago by Jalil Sharif ▴ 80
6
votes
12
replies
2.2k
views
6 follow
gtf2bed not converting to bed
bed gtf
updated 14 months ago by 8.6k • written 14 months ago by ▴ 80
3
votes
4
replies
786
views
Ensembl equivalent of refseq transcript fasta
ensembl transcriptome refseq
14 months ago by Jalil Sharif ▴ 80
0
votes
1
reply
902
views
short read aligners 25-50bp BWA vs BWA-MEM vs Bowtie vs Bowtie2
alignment read short
updated 15 months ago by 6.4k • written 15 months ago by ▴ 80
0
votes
2
replies
741
views
differential gene expression pipelines rnaflow vs rnaseq
differential expression gene
15 months ago by Jalil Sharif ▴ 80
0
votes
0
replies
407
views
bowtie2 code to bwa-mem2
bwa-mem2 bowtie2
16 months ago by Jalil Sharif ▴ 80
1
vote
1
reply
1.4k
views
Extracting Beta, SE and P-Value from GLM model
beta glm r
updated 22 months ago by 3.9k • written 22 months ago by ▴ 80
0
votes
1
reply
430
views
Annotation SNP's with their Gene names
Gene annotations
updated 24 months ago by 2.8k • written 24 months ago by ▴ 80
0
votes
0
replies
414
views
PLINK - PRS/GRS .fam file has fewer tokens
plink fam PRS
updated 14 months ago by 43k • written 2.1 years ago by ▴ 80
1
vote
3
replies
835
views
How to find top-hit SNP from gwas.
SNP GWAS tophits
2.2 years ago by Jalil Sharif ▴ 80
0
votes
3
replies
2.5k
views
Clumping error Plink
clumping plink biobank uk
updated 2.3 years ago by ★ 4.7k • written 2.3 years ago by ▴ 80
0
votes
2
replies
972
views
UK Biobank difference in number of patients diagnosed in field 41270 vs extracted phenotypes.
Field Diagnosis UK Biobank
2.3 years ago by Jalil Sharif ▴ 80
4
votes
5
replies
1.2k
views
Averaging across multiple columns
awk bash column
2.5 years ago by Jalil Sharif ▴ 80
4
votes
6
replies
6.8k
views
merging multiple .bed /.bgen files uk biobank using plink
plink uk biobank merge-list
2.5 years ago by Jalil Sharif ▴ 80
1
vote
15
replies
4.2k
views
PRS in UK Biobank - no covariate file and no phenotype file
UK Biobank PRS
2.6 years ago by Jalil Sharif ▴ 80
0
votes
0
replies
1.1k
views
[gatk 3.6.0] GVCF - haplotypecaller - cross referencing multiple VCF
GVCF haplotypecaller vcf
3.9 years ago by Jalil Sharif ▴ 80
0
votes
0
replies
717
views
[gatk 3.6] Haplotypecaller & RealignerTargetCreator
haplotypecaller realignment
3.9 years ago by Jalil Sharif ▴ 80
23 results • Page 1 of 1
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