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823 results • Page
1 of 17
Sort: Views
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Views
Votes
Replies
362
votes
82
replies
143k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 2 days ago by
jena
▴ 290 • written 11.1 years ago by
ole.tange
★ 4.4k
105
votes
15
replies
111k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 7 days ago by
xiaoleiusc
▴ 140 • written 11.8 years ago by
GouthamAtla
12k
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 8 days ago by
Michael
54k • written 14.0 years ago by
Yuri
★ 1.7k
66
votes
23
replies
48k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 11 days ago by
Getnet Tesfaw
• 0 • written 6.3 years ago by
1769mkc
★ 1.2k
78
votes
38
replies
32k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 27 days ago by
nickp60
▴ 60 • written 7.8 years ago by
andrew.j.skelton73
6.5k
103
votes
42
replies
30k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 19 days ago by
Jeremy Leipzig
22k • written 10.4 years ago by
14134125465346445
★ 3.6k
41
votes
13
replies
25k
views
13 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq
DESeq2
geneontology
GSEA
updated 20 days ago by
CTLong
▴ 90 • written 6.4 years ago by
Sreeraj Thamban
▴ 290
26
votes
5
replies
23k
views
BLAST options: max_target_seqs and num_alignments
blast
updated 7 days ago by
Lada
▴ 30 • written 9.4 years ago by
biolab
★ 1.4k
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 9 days ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
5
votes
7
replies
19k
views
6 follow
VCF To FASTA
next-gen
genetic
genome
updated 19 days ago by
seta
★ 1.9k • written 5.2 years ago by
Myo Naung
▴ 10
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 4 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression
RNA-Seq
DESeq2
updated 8 days ago by
Bionaught
• 0 • written 5.7 years ago by
firestar
★ 1.6k
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 21 days ago by
barslmn
★ 2.1k • written 6.6 years ago by
a.rex
▴ 350
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 14 days ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
46
votes
13
replies
14k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 16 days ago by
Konstantinos
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
12
votes
19
replies
14k
views
11 follow
SnpMatrix from VCF file
VCF
Eqtl
MatrixEQTL
SnpMatrix
vcftools
updated 13 days ago by
pmiller
▴ 10 • written 7.0 years ago by
Dhana
▴ 110
8
votes
12
replies
13k
views
11 follow
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
updated 25 days ago by
BioinfGuru
★ 1.6k • written 4.0 years ago by
chatterjee.arumoy
▴ 50
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 3 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
0
votes
3
replies
12k
views
Converting PDBQT output to PDB in VINA
Docking
PDBQT
VINA
updated 21 days ago by
Ricard
• 0 • written 8.3 years ago by
marawanhussain
▴ 30
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 2 days ago by
Ram
43k • written 13.5 years ago by
toshnam
▴ 650
14
votes
9
replies
11k
views
8 follow
Downsample BAM file to specific amount of reads
bam
updated 13 days ago by
GenoMax
140k • written 2.6 years ago by
kstangline
▴ 80
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 2 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
16
votes
10
replies
10k
views
8 follow
GRCh37.p13 download at NCBI FTP?
ncbi
reference
grch37
updated 18 days ago by
Sruthi
• 0 • written 5.5 years ago by
Marvin
▴ 220
21
votes
26
replies
9.4k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 13 days ago by
Yao
▴ 30 • written 4.3 years ago by
Juke34
8.5k
82
votes
46
replies
8.3k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 14 days ago by
LauferVA
4.1k • written 9 months ago by
Sasha
▴ 830
25
votes
15
replies
7.6k
views
9 follow
Randomize Read Order In Multigbp Fastq File?
fastq
updated 16 days ago by
Cliff
• 0 • written 12.7 years ago by
2184687-1231-83-
★ 5.1k
15
votes
10
replies
7.5k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 20 hours ago by
Alex Reynolds
35k • written 8.2 years ago by
int11ap1
▴ 470
8
votes
7
replies
6.8k
views
Parse the Xml response from Entrez Db=bioproject Using Biopython eFetch
entrez
efetch
biopython
xml
updated 7 days ago by
LauferVA
4.1k • written 8.8 years ago by
Prasad
▴ 50
12
votes
7
replies
6.7k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 3 days ago by
dsull
★ 5.7k • written 2.6 years ago by
hamarillo
▴ 70
3
votes
8
replies
6.2k
views
6 follow
Download CAZy database
genome
gene
database
cazy
updated 13 days ago by
GenoMax
140k • written 6.1 years ago by
anu014
▴ 190
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 1 day ago by
Tania
• 0 • written 6.8 years ago by
Tom_L
▴ 350
7
votes
15
replies
5.5k
views
9 follow
convert VCF to gVCF
gVCF
VCF
updated 20 days ago by
jena
▴ 290 • written 4.5 years ago by
mateid
• 0
5
votes
5
replies
5.4k
views
beagle 4 exception: Duplicate marker
vcf
IBD
plink
beagle
updated 1 day ago by
Ram
43k • written 9.3 years ago by
galbarel
▴ 10
8
votes
16
replies
5.2k
views
9 follow
visualize CNV data based on WGS
CNV
updated 7 days ago by
clealk
▴ 50 • written 6.2 years ago by
Bogdan
★ 1.4k
18
votes
10
replies
5.2k
views
Should I normalize read counts if I want to run plotPCA?
RNA-Seq
updated 19 days ago by
ella
• 0 • written 3.9 years ago by
c_u
▴ 520
12
votes
19
replies
5.2k
views
how to identify CDR region in antibody sequence
CDR
antibody
updated 27 days ago by
tiancheng
• 0 • written 21 months ago by
reany
▴ 50
11
votes
8
replies
5.0k
views
Multi-mapping High with featureCounts but not STAR
RNA-Seq
sequencing
alignment
updated 7 days ago by
GenoMax
140k • written 4.8 years ago by
garbuzov
▴ 70
17
votes
8
replies
5.0k
views
Mean Variance Relationship single cell RNA-Seq Data
RNA-Seq
variance
deseq2
single cell
updated 16 days ago by
thomas.heigl.ibk
• 0 • written 3.3 years ago by
kw486
▴ 30
5
votes
15
replies
4.7k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 5 days ago by
vague-barracuda-4686
• 0 • written 4.7 years ago by
Apprentice
▴ 160
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 21 hours ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
9
votes
1
reply
4.4k
views
How To Generate Synthetic Read Data From An Existing Fasta
fasta
sequence
reads
updated 22 days ago by
Ram
43k • written 10.2 years ago by
smith.tracymae
• 0
9
votes
6
replies
4.4k
views
6 follow
Remove contigs that are lower than 200
assembly
sequencing
genome
next-gen
updated 19 days ago by
GenoMax
140k • written 4.1 years ago by
Bioinfo
▴ 20
2
votes
2
replies
4.3k
views
Variant calling for sanger reads
variant-calling
sanger
alignment
variants
updated 2 days ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
3
votes
12
replies
4.2k
views
samtools mpileup keeps making an empty file
samtools
pileup
updated 27 days ago by
gabt
▴ 120 • written 5.2 years ago by
James Reeve
▴ 130
10
votes
6
replies
4.0k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 1 day ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
4
votes
14
replies
4.0k
views
Trouble with bedtools getfasta
bedtools
getfasta
written 2.1 years ago by
gkunz
▴ 30
5
votes
9
replies
3.7k
views
Can one plot % of variance using the plotMDS function?
limma
plotMDS
PCA
PCoA
% of varience
updated 26 days ago by
Gordon Smyth
★ 6.9k • written 3.8 years ago by
harelarik
▴ 90
2
votes
4
replies
3.6k
views
Tutorial for analysing gpr files of microarray
GPR
microarray
updated 6 days ago by
bioyas
▴ 10 • written 5.4 years ago by
afli
▴ 190
12
votes
7
replies
3.6k
views
6 follow
Convert FPKM to TPM in R
r
TPM
normalization
meta-analysis
updated 29 days ago by
Ram
43k • written 18 months ago by
JACKY
▴ 130
4
votes
12
replies
3.4k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 2 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
823 results • Page
1 of 17
Recent Votes
How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis?
Comment: Only one read per run - Trying to use CellRangerv7
Comment: Interproscan taking so much time
Answer: Interproscan taking so much time
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
A: Crispr-cas9 screen analysis mageck
A: Crispr-cas9 screen analysis mageck
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104k
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amitpande74
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160k
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Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did ran the `JoinLayers()` even then it is not working, here is the output before and after ```r DefaultAssay(combined1) <- 'RNA' com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I tried that too. It did not work.
Comment: (sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
by
GenoMax
140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
Comment: Issue with making local BLAST database
by
Begonia_pavonina
▴ 140
Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
Comment: Nanopore data filtering using fastp
by
GenoMax
140k
You can also use `reformat.sh` from [**BBMap suite**][1]. Look at sampling options. [1]: https://sourceforge.net/projects/bbmap/
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I was using it but the output file was too big pipe the output
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Share code and an example please.
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
Comment: Interproscan taking so much time
by
Mohamed Abderrahmane
▴ 10
Thank you for your reply. I have just executed the computation with parallelization as you mentioned, and I will observe the differences. H…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
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