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2
votes
2
replies
219
views
Is refSeq table DNA or RNA coordinate?
RefSeq
UCSC
NCBI
updated 4 weeks ago by
GenoMax
142k • written 4 weeks ago by
Alewa
▴ 170
11
votes
3
replies
768
views
is oxford nanopore technology data paired or single end sequencing?
oxford-nanopore
DNA
RNA
updated 3 months ago by
Ram
43k • written 3 months ago by
Alewa
▴ 170
0
votes
0
replies
521
views
Comment:
Comment: should I use normalized counts or transformed of normalized counts for RNA-seq a
6 months ago by
Alewa
▴ 170
1
vote
2
replies
521
views
should I use normalized counts or transformed of normalized counts for RNA-seq association analysis?
methylation
DESeq
RNA-Seq
6 months ago by
Alewa
▴ 170
1
vote
0
replies
323
views
how to get genomic locations of Sequence patterns in R
R
GenomicRanges
Biostrings
bioconductor
6 months ago by
Alewa
▴ 170
1
vote
0
replies
576
views
Comment:
Comment: bedtools intersect by position & stand not working even with common regions
7 months ago by
Alewa
▴ 170
2
votes
2
replies
576
views
bedtools intersect by position & stand not working even with common regions
bedtools
genomic
intersect
bedops
intervals
7 months ago by
Alewa
▴ 170
4
votes
3
replies
800
views
count number of GC for a given genomic ranges
bsgenome
biostrings
epigenetics
updated 9 months ago by
ATpoint
82k • written 9 months ago by
Alewa
▴ 170
0
votes
1
reply
643
views
bioconductor caches fails to load/corrupted for annotation databases
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocFileCache
AnnotationDbi
R
updated 10 months ago by
Ram
43k • written 10 months ago by
Alewa
▴ 170
1
vote
0
replies
405
views
Answer:
Answer: plyranges:: summarise() not recognizing previous summarized column (counts)
11 months ago by
Alewa
▴ 170
1
vote
1
reply
405
views
plyranges:: summarise() not recognizing previous summarized column (counts)
cpg
R
plyranges
11 months ago by
Alewa
▴ 170
0
votes
0
replies
686
views
Comment:
Comment: how to intersect multiple bed files and get results in uncollapsed genomic inter
11 months ago by
Alewa
▴ 170
1
vote
2
replies
686
views
how to intersect multiple bed files and get results in uncollapsed genomic intervals
bedtools
bedops
updated 10 months ago by
Ram
43k • written 11 months ago by
Alewa
▴ 170
0
votes
1
reply
450
views
How to find complete overlaps between between multiple .bed files with bedtools
bedtools
granges
updated 11 months ago by
Pierre Lindenbaum
161k • written 11 months ago by
Alewa
▴ 170
0
votes
0
replies
1.0k
views
Comment:
Comment: chromosome start & end for genes in biomart R not showing
16 months ago by
Alewa
▴ 170
0
votes
0
replies
1.0k
views
Comment:
Comment: chromosome start & end for genes in biomart R not showing
16 months ago by
Alewa
▴ 170
3
votes
5
replies
1.0k
views
chromosome start & end for genes in biomart R not showing
ensembl
bioconductor
biomart
updated 16 months ago by
Ram
43k • written 16 months ago by
Alewa
▴ 170
1
vote
0
replies
1.6k
views
Comment:
Comment: where to find mouse genome GRCm38/mm10 for biomart R
16 months ago by
Alewa
▴ 170
4
votes
2
replies
1.6k
views
where to find mouse genome GRCm38/mm10 for biomart R
ensembl
bioconductor
mouse
biomart
16 months ago by
Alewa
▴ 170
0
votes
1
reply
1.7k
views
Comment:
Comment: gene symbol not showing for ensembl gene ids using biomart
16 months ago by
Alewa
▴ 170
5
votes
5
replies
1.7k
views
gene symbol not showing for ensembl gene ids using biomart
ensembl
biomart
bioconductor
refseq
updated 16 months ago by
Ram
43k • written 16 months ago by
Alewa
▴ 170
0
votes
0
replies
569
views
Comment:
Comment: How to insert quotes around description of format field in vcf header?
22 months ago by
Alewa
▴ 170
2
votes
2
replies
569
views
How to insert quotes around description of format field in vcf header?
vcf
bcftools
22 months ago by
Alewa
▴ 170
0
votes
0
replies
702
views
Comment:
Comment: How is contig length calculated ?
22 months ago by
Alewa
▴ 170
3
votes
2
replies
702
views
How is contig length calculated ?
tuberculosis
Contig
assembly
Genome
Mycobacterium
22 months ago by
Alewa
▴ 170
0
votes
1
reply
745
views
Comment:
Comment: Why are number of CDS smaller than corresponding genes [M. tb]
23 months ago by
Alewa
▴ 170
4
votes
3
replies
745
views
Why are number of CDS smaller than corresponding genes [M. tb]
NCBI
entrez
bash
genes
updated 23 months ago by
Joe
21k • written 23 months ago by
Alewa
▴ 170
0
votes
0
replies
517
views
Comment:
Comment: [out of memory issue] NCBI Entrez protein seq download
23 months ago by
Alewa
▴ 170
2
votes
2
replies
517
views
[out of memory issue] NCBI Entrez protein seq download
NCBI
entrez
bash
protein
23 months ago by
Alewa
▴ 170
10
votes
5
replies
4.8k
views
How to generate start & end coordinates for each chromosome of human ref genome in bed. format (0-based index)
bed
bedtools
bioconductor
genome
updated 2.8 years ago by
Jorge Amigo
14k • written 4.1 years ago by
Alewa
▴ 170
0
votes
0
replies
1.7k
views
Comment:
Comment: Segmentation fault in bcftools while changing the sample names
3.1 years ago by
Alewa
▴ 170
0
votes
0
replies
716
views
How to covert VCF-like to ICGC-like vcf Format
conversion
annotation
3.1 years ago by
Alewa
▴ 170
0
votes
0
replies
4.3k
views
Comment:
C: [GRanges] How to append query metadata to subjectHits
3.4 years ago by
Alewa
▴ 170
4
votes
2
replies
4.3k
views
[GRanges] How to append query metadata to subjectHits
R
granges
bioconductor
findOverlaps
updated 3.4 years ago by
Papyrus
★ 2.9k • written 3.4 years ago by
Alewa
▴ 170
0
votes
1
reply
1.6k
views
Comment:
A: Convert list of ensembl Human genes -GRCh38.p13- from biomart to hg38 coordinate
3.7 years ago by
Alewa
▴ 170
0
votes
3
replies
1.6k
views
Convert list of ensembl Human genes -GRCh38.p13- from biomart to hg38 coordinates
Ensembl
genome
hg38
assembly
liftover
3.7 years ago by
Alewa
▴ 170
5
votes
0
replies
2.2k
views
Answer:
A: what is the difference between calling variants with and without interval list?
3.7 years ago by
Alewa
▴ 170
0
votes
0
replies
855
views
filtered and dropped vcfs empty when filtering 1000 gemomes variants with Annova
germline
annovar
1000genomes
annotation
3.7 years ago by
Alewa
▴ 170
2
votes
0
replies
2.8k
views
Answer:
C: [R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserv
3.9 years ago by
Alewa
▴ 170
0
votes
1
reply
2.8k
views
Comment:
C: [R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserv
3.9 years ago by
Alewa
▴ 170
2
votes
4
replies
2.8k
views
[R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserved words. this is not the case
R
GenomicRanges
bioconductor
updated 3.9 years ago by
Kevin Blighe
87k • written 3.9 years ago by
Alewa
▴ 170
1
vote
0
replies
1.9k
views
Answer:
A: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
3.9 years ago by
Alewa
▴ 170
1
vote
5
replies
1.9k
views
Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped) ]
SNP
bash
vcf
bcftools
gatk
3.9 years ago by
Alewa
▴ 170
0
votes
0
replies
1.7k
views
[R] subsetByOverlaps (Granges list and Granges object) not giving specific hits
R
GenomicFeatures
bioconductor
3.9 years ago by
Alewa
▴ 170
0
votes
1
reply
1.9k
views
Comment:
A: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
4.1 years ago by
Alewa
▴ 170
0
votes
0
replies
1.9k
views
Comment:
C: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
4.1 years ago by
Alewa
▴ 170
0
votes
0
replies
1.6k
views
Comment:
C: how to concetanate column values of a data frame and converting single letters o
4.1 years ago by
Alewa
▴ 170
1
vote
0
replies
4.8k
views
Comment:
C: How to generate start & end coordinates for each chromosome of human ref genome
4.1 years ago by
Alewa
▴ 170
0
votes
0
replies
1.4k
views
Answer:
A: Somatic mutations per gene
4.3 years ago by
Alewa
▴ 170
0
votes
1
reply
2.0k
views
Comment:
C: db-GaP / GTEx analysis on the cloud. Easiest way?
4.5 years ago by
Alewa
▴ 170
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