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1,000 results • Page 2 of 20
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43
votes
15
replies
87k
views
9 follow
How Do I Count The Number Values Less Than X In A Column Using R ?
rna edger r counts
updated 9.5 years ago by 11k • written 13.1 years ago by ▴ 920
163
votes
64
replies
87k
views
39 follow
Selecting Random Pairs From Fastq?
random fastq illumina sequence
updated 3 months ago by 43k • written 13.2 years ago by 4.1k
108
votes
45
replies
87k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 20 months ago by ▴ 80 • written 11.8 years ago by ▴ 320
19
votes
14
replies
86k
views
10 follow
BLAST Database error: No alias or index file found for nucleotide database
blast blastn sift makeblastdb
updated 7 months ago by • 0 • written 9.6 years ago by ▴ 320
128
votes
24
replies
85k
views
18 follow
Sequence Length Distribution From A Fastq File
sequence length fastq
updated 5.0 years ago by • 0 • written 11.0 years ago by ▴ 380
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram visualization chromosome
updated 8 weeks ago by 54k • written 14.2 years ago by ★ 1.7k
106
votes
12
replies
80k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools intersect
updated 19 months ago by 43k • written 12.6 years ago by ★ 1.7k
120
votes
8
replies
80k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi ucsc grch38 hg38
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 540
33
votes
4
replies
79k
views
7 follow
Merging Bam Files
picard samtools
updated 5.0 years ago by ▴ 60 • written 12.4 years ago by ▴ 180
60
votes
15
replies
78k
views
9 follow
BAM/SAM to FASTA conversion
sam bam
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 1.4k
100
votes
16
replies
78k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq coverage
9.5 years ago by Obi Griffith 20k
27
votes
2
replies
77k
views
How Can I Make A Bed File?
bed
updated 12.7 years ago by ▴ 300 • written 12.7 years ago by ▴ 580
122
votes
17
replies
76k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 2.2 years ago by 43k • written 13.1 years ago by ▴ 370
20
votes
2
replies
74k
views
Subsetting in R based on row name?
R
updated 8.1 years ago by 104k • written 8.1 years ago by ▴ 80
51
votes
18
replies
74k
views
10 follow
Extract User Defined Region From An Fasta File
sequence fasta
updated 6.8 years ago by ▴ 30 • written 12.8 years ago by ▴ 290
188
votes
50
replies
74k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta sequence duplicates
updated 19 months ago by 43k • written 13.6 years ago by ▴ 340
68
votes
18
replies
73k
views
17 follow
Project For A Beginner Bioinformatics Student
project java
updated 22 months ago by 43k • written 12.5 years ago by ▴ 240
43
votes
25
replies
73k
views
10 follow
Will A Masters In Bioinformatics Help Me In Getting A Job?
career education
updated 13.1 years ago by ★ 1.4k • written 13.1 years ago by ▴ 50
54
votes
17
replies
73k
views
11 follow
Extract fasta sequences from a file using a list in another file.
fasta header extract awk grep
updated 3.4 years ago by ▴ 470 • written 6.0 years ago by ▴ 50
237
votes
45
replies
72k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen sequencing illumina exome human
updated 12.9 years ago by ▴ 50 • written 14.0 years ago by 5.0k
19
votes
8
replies
72k
views
6 follow
Pheatmap Annotation
r heatmap
updated 8.8 years ago by ▴ 560 • written 11.2 years ago by ▴ 80
138
votes
21
replies
71k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer gene database oncogene tumor
3.6 years ago by Malachi Griffith 20k
42
votes
14
replies
71k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 2.0 years ago by 43k • written 13.4 years ago by ▴ 250
33
votes
17
replies
71k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray heatmap
updated 16 months ago by 43k • written 13.0 years ago by ▴ 80
93
votes
18
replies
71k
views
12 follow
Sequence length from Fasta
fasta
updated 17 months ago by 43k • written 9.5 years ago by ▴ 80
1
vote
3
replies
70k
views
Error in loading R package "GO.db" in installing WGCNA R package
R
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 10
12
votes
9
replies
70k
views
7 follow
combining fasta files
windows fasta notepad
updated 18 months ago by • 0 • written 9.3 years ago by ▴ 30
40
votes
15
replies
70k
views
14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix conversion entrez
updated 19 months ago by 43k • written 10.9 years ago by ▴ 140
116
votes
25
replies
70k
views
14 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 15 months ago by ▴ 20 • written 13.3 years ago by 161k
56
votes
4
replies
69k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence next-gen-sequencing
updated 19 months ago by 43k • written 9.5 years ago by ▴ 800
51
votes
15
replies
69k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts sequence fastq
updated 15 months ago by 43k • written 12.9 years ago by ★ 1.7k
35
votes
9
replies
69k
views
8 follow
Minor allele frequency calculation
SNP next-gen
updated 24 months ago by 43k • written 9.5 years ago by ▴ 50
9
votes
6
replies
69k
views
How To Calculate Coverage
fastq coverage
updated 10.3 years ago by ▴ 90 • written 10.3 years ago by ★ 1.2k
20
votes
15
replies
69k
views
12 follow
Python Script To Translate Rna Sequences To Protein Sequences
python biopython translation
updated 10.7 years ago by ▴ 50 • written 13.6 years ago by ▴ 70
51
votes
15
replies
68k
views
15 follow
Any Recommendations For Software For Drawing Plasmid Maps?
visualization software
updated 2.1 years ago by 43k • written 12.9 years ago by ▴ 70
24
votes
23
replies
68k
views
7 follow
Multiple Histograms In One Plot
r
updated 2.4 years ago by 43k • written 10.9 years ago by ★ 1.8k
1
vote
2
replies
67k
views
"SyntaxError: unexpected EOF while parsing " IN PYTHON 3.7
PYTHON
updated 3.1 years ago by 100k • written 4.0 years ago by • 0
141
votes
33
replies
67k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 18 months ago by 43k • written 10.1 years ago by ▴ 510
138
votes
22
replies
66k
views
15 follow
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene LIMMA edgeR
updated 11 months ago by 88k • written 6.5 years ago by ★ 1.9k
13
votes
13
replies
65k
views
pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R RNA-Seq pheatmap arg10
updated 3.4 years ago by ▴ 40 • written 3.9 years ago by ▴ 160
63
votes
22
replies
65k
views
16 follow
How To Convert Gencode Gtf Into Bed Format ?
gtf bed
updated 17 months ago by • 0 • written 11.5 years ago by ★ 1.5k
328
votes
54
replies
64k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 6 months ago by 43k • written 14.2 years ago by 24k
31
votes
11
replies
64k
views
samtools sort bam file
ChIP-Seq
updated 5.9 years ago by 47k • written 5.9 years ago by ▴ 120
40
votes
7
replies
63k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r rna heatmap clustering gene
updated 23 months ago by 43k • written 12.5 years ago by ▴ 450
17
votes
14
replies
63k
views
7 follow
Convert SAM to BAM
sam RNA-Seq bam
updated 2.4 years ago by 43k • written 9.8 years ago by ▴ 90
1
vote
6
replies
63k
views
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
R
updated 14 months ago by 43k • written 7.4 years ago by • 0
102
votes
6
replies
63k
views
6 follow
Insert Size And Fragment Size ?
2.5 years ago by Nicolas Rosewick 11k
36
votes
14
replies
63k
views
9 follow
What Is The Difference Between Hg18 And Hg19?
genome hg hg
updated 12.3 years ago by 14k • written 12.3 years ago by ▴ 170
159
votes
24
replies
63k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing splicing rna-seq
updated 11 months ago by 43k • written 11.2 years ago by 11k
39
votes
20
replies
63k
views
8 follow
How to convert to .SRA files to .FQ (FASTQ)
fastq FASTQ sra RNA-Seq SRAA
updated 2.3 years ago by ▴ 20 • written 9.8 years ago by ▴ 50
1,000 results • Page 2 of 20
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Recent Replies
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
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