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1,000 results • Page
4 of 20
Sort: Views
Rank
Views
Votes
Replies
76
votes
22
replies
52k
views
17 follow
How To Download All Sra Samples At Once ?
geo
sra
updated 6 months ago by
Ram
40k • written 9.6 years ago by
biorepine
★ 1.5k
49
votes
13
replies
52k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 2 days ago by
camillab.
▴ 140 • written 7.7 years ago by
nash.claire
▴ 490
40
votes
9
replies
52k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen
RNA-Seq
single-cell
R
updated 8 weeks ago by
camillab.
▴ 140 • written 3.8 years ago by
Payal
▴ 140
29
votes
11
replies
51k
views
samtools sort bam file
ChIP-Seq
updated 5.3 years ago by
WouterDeCoster
47k • written 5.3 years ago by
mikysyc2016
▴ 120
50
votes
33
replies
51k
views
10 follow
I would like to add gene names to a volcano plot obtained from DEseq2
RNA-Seq
DEseq2
R
updated 5.4 years ago by
Kevin Blighe
86k • written 7.2 years ago by
ta_awwad
▴ 340
48
votes
19
replies
51k
views
11 follow
How Can I Convert Bam/Sam To Wiggle
wiggle
perl
samtools
updated 6 months ago by
Ram
40k • written 13.0 years ago by
Stew
★ 1.4k
10
votes
5
replies
51k
views
Finding number of duplicates in R
R
updated 7.1 years ago by
keith.hughitt
▴ 280 • written 7.1 years ago by
nkabo
▴ 70
16
votes
14
replies
50k
views
7 follow
Convert SAM to BAM
sam
RNA-Seq
bam
updated 22 months ago by
Ram
40k • written 9.2 years ago by
marina-orlova
▴ 90
87
votes
25
replies
50k
views
21 follow
How To Split A Multiple Fasta
fasta
split
updated 20 months ago by
Ram
40k • written 13.1 years ago by
Gvj
▴ 470
89
votes
21
replies
50k
views
13 follow
Should We Remove Duplicated Reads In Rna-Seq ?
rna-seq
read
updated 9.8 years ago by
earonesty
▴ 250 • written 10.9 years ago by
siddharth.sethi5
▴ 270
22
votes
4
replies
50k
views
Convert VCFf file to plink ped/map format while filtering the SNPs
vcftools
plink
ped
map
updated 4.6 years ago by
hakimeazarafra
• 0 • written 9.0 years ago by
roll
▴ 350
98
votes
12
replies
50k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl
entrez
gene
updated 2.5 years ago by
hagenaue
▴ 10 • written 11.7 years ago by
Untom
▴ 420
30
votes
20
replies
50k
views
11 follow
List Of All Transcription Factors In Human
transcription
ensembl
genes
updated 11.0 years ago by
Alex Reynolds
35k • written 11.0 years ago by
dfernan
▴ 750
0
votes
3
replies
50k
views
Tutorial:
Installation VMD on LINUX_64
gromacs
VMD
updated 5 months ago by
Ram
40k • written 7.3 years ago by
Hassan Rasouli
▴ 10
37
votes
8
replies
50k
views
10 follow
Adding Read Groups To Bam Files
bam
gatk
samtools
bwa
updated 2.3 years ago by
zx8754
11k • written 11.3 years ago by
Zev.Kronenberg
12k
36
votes
4
replies
50k
views
TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
z-scores
TCGA
RSEM
updated 2.5 years ago by
Ram
40k • written 9.2 years ago by
komal.rathi
★ 4.1k
87
votes
37
replies
49k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 18 months ago by
Ram
40k • written 10.2 years ago by
Hunter
▴ 110
6
votes
7
replies
49k
views
matching and merging data frames of different lengths
R
updated 24 months ago by
Ram
40k • written 9.3 years ago by
Diana
▴ 900
60
votes
15
replies
49k
views
11 follow
Estimate Insert Size In Paired-End/Mate-Pair
next-gen
sequencing
alignment
paired
updated 23 months ago by
Ram
40k • written 11.7 years ago by
Ric
▴ 190
24
votes
7
replies
49k
views
What Databases Are Available For Rna-Seq Datasets?
rna-seq
database
geo
updated 11.3 years ago by
Khader Shameer
18k • written 11.3 years ago by
aprathke
▴ 140
45
votes
3
replies
49k
views
Gwas Vs. Qtl Mapping?
gwas
mapping
updated 15 months ago by
Ram
40k • written 11.3 years ago by
Justin
▴ 460
10
votes
4
replies
49k
views
BLAST: Identity % and Similarity %
blast
updated 7.3 years ago by
natasha.sernova
★ 3.9k • written 7.3 years ago by
hnp21
▴ 40
16
votes
8
replies
49k
views
9 follow
Ensembl Ids To Gene Name Conversion
gene
ensembl
updated 4.6 years ago by
liangj
• 0 • written 11.4 years ago by
jill.mckay
▴ 30
57
votes
15
replies
48k
views
11 follow
Filtering Vcf File
vcftools
vcf
snp
indel
updated 19 months ago by
Ram
40k • written 11.1 years ago by
bioinfo
▴ 830
66
votes
19
replies
48k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 3 months ago by
Ram
40k • written 10.6 years ago by
14134125465346445
★ 3.6k
88
votes
52
replies
48k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq
pca
updated 22 months ago by
BioNovice247
▴ 10 • written 5.9 years ago by
rachel.kubik12
▴ 210
35
votes
5
replies
48k
views
Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about that in an assymmetrical matrix
pheatmap
R
updated 7 months ago by
Ram
40k • written 6.6 years ago by
emil.bb
▴ 180
65
votes
9
replies
48k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
reference
samtools
mapping
bwa
updated 7 months ago by
Ram
40k • written 10.3 years ago by
Joseph Hughes
★ 3.0k
4
votes
1
reply
48k
views
In ggplot, assign a variable/category to a specific color?
R
ggplot
plots
colors
updated 7.0 years ago by
Biostar
20 • written 7.2 years ago by
james.lloyd
▴ 100
29
votes
9
replies
48k
views
What Is The Difference Between Sequencing Depth And Coverage
sequencing
read
coverage
updated 12.5 years ago by
Michael
53k • written 12.5 years ago by
User 6659
▴ 970
46
votes
15
replies
48k
views
11 follow
How to extract specific chromosome from vcf file
vcf
updated 12 months ago by
beausoleilmo
▴ 550 • written 7.2 years ago by
MAPK
★ 2.0k
41
votes
16
replies
48k
views
10 follow
How to split paired end SRA file into 2 correct fastq files
next-gen
sra
fastq
updated 19 months ago by
Alejandro Miguel
▴ 10 • written 6.9 years ago by
thustar
▴ 130
13
votes
5
replies
48k
views
7 follow
Obtaining The Snp Rs Number With The Chromosomal Position
r
snps
bioconductor
updated 2.0 years ago by
krassowski.michal
▴ 180 • written 10.4 years ago by
Sheila
▴ 410
29
votes
10
replies
47k
views
How To Check If Illumina Fastq Is Single Or Paired End With Minimal Sequence Id
fastq
paired-end
illumina
updated 9.5 years ago by
Chris Fields
★ 2.2k • written 9.6 years ago by
fbrundu
▴ 330
21
votes
11
replies
47k
views
reading a bed file in R
bed
R
updated 22 months ago by
Ram
40k • written 7.8 years ago by
fi1d18
★ 4.2k
52
votes
21
replies
47k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 3 months ago by
Ram
40k • written 11.5 years ago by
Geparada
★ 1.5k
41
votes
7
replies
47k
views
How to extract sample id using bcftools or vcftools
SNP
vcf
bcftools
vcftools
updated 2.2 years ago by
Ömer An
▴ 260 • written 8.4 years ago by
xinhui.wang
▴ 520
23
votes
5
replies
47k
views
Any Method Of Converting Bigwig File Format Into Bed Format?
bigwig
bed
updated 4.3 years ago by
Samir
▴ 200 • written 10.4 years ago by
samwise.techno
▴ 50
146
votes
70
replies
46k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 4 weeks ago by
Raheleh
▴ 260 • written 5.9 years ago by
Kevin Blighe
86k
27
votes
15
replies
46k
views
16 follow
how to unzip the files in batch?
next-gen
RNA-Seq
SNP
alignment
updated 8 months ago by
Ram
40k • written 8.4 years ago by
flavobacteria
▴ 50
125
votes
46
replies
46k
views
21 follow
Forum:
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization
ChIP-Seq
homer
ngsplot
deeptools
updated 5 months ago by
Ram
40k • written 7.6 years ago by
Sinji
★ 3.2k
54
votes
52
replies
46k
views
12 follow
Tool:
Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF
Gene-Clustering
updated 3 months ago by
Ram
40k • written 9.2 years ago by
EagleEye
7.5k
4
votes
1
reply
46k
views
ggmaplot error: Unlabeled data points (too many overlaps). Consider increasing max.overlaps
MAplot
r
ggplot2
ggmaplot
updated 2.2 years ago by
ATpoint
77k • written 2.7 years ago by
jaqx008
▴ 110
112
votes
24
replies
45k
views
17 follow
Workflow Or Tutorial For Snp Calling?
snp
samtools
alignment
next-gen
sequencing
updated 13 months ago by
Ram
40k • written 12.4 years ago by
Matthieu
▴ 480
30
votes
10
replies
45k
views
Filtering A Sam File For Quality Scores
sam
updated 11.4 years ago by
Sukhi Singh
11k • written 11.4 years ago by
Varun Gupta
★ 1.3k
2
votes
5
replies
45k
views
Convert text file to VCF file ?
vcf
updated 3 months ago by
Ram
40k • written 8.6 years ago by
CrazyB
▴ 260
32
votes
19
replies
45k
views
11 follow
Convert Refseq Id To Gene Name
refseq
gene
updated 11 weeks ago by
Ram
40k • written 10.3 years ago by
hicsuntdrac0nis
▴ 240
61
votes
22
replies
45k
views
7 follow
extract dendrogram cluster from pheatmap
R
updated 19 months ago by
mirkocelii
• 0 • written 5.8 years ago by
1769mkc
★ 1.1k
44
votes
11
replies
45k
views
7 follow
In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
seurat
single-cell
updated 23 months ago by
jared.andrews07
★ 15k • written 3.9 years ago by
bioinformatics2020
▴ 770
49
votes
4
replies
45k
views
How To Convert The Bed File To Ped File
bed
ped
updated 13 months ago by
sonsunjirachote
• 0 • written 13.1 years ago by
Austinlew
▴ 310
1,000 results • Page
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Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
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Comment: ncbi error report log for validate fastq issue
A: Bowtie2 MAPQ difference using local vs end-to-end alignment
C: Bowtie2 MAPQ difference using local vs end-to-end alignment
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Comment: Weirdness in annotation (missing allele frequencies)
by
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Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
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• 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
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134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
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I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
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bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
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Answer: Search RCSB with a list of protein names?
by
Mensur Dlakic
★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
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The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools
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Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
• 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
This is a really neat package, but I don't think it does exactly what I want, so I've clarified my question. This seems like it grabs a PD…
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