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1,000 results • Page 1 of 20
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226
votes
39
replies
289k
views
33 follow
Gene Id Conversion Tool
david
updated 7 months ago by 43k • written 14.6 years ago by ▴ 620
334
votes
92
replies
241k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 9 months ago by ▴ 190 • written 13.3 years ago by 5.0k
120
votes
31
replies
200k
views
17 follow
Correct Way To Parse A Fasta File In Python
python fasta
updated 6 months ago by 43k • written 14.1 years ago by 11k
124
votes
13
replies
174k
views
13 follow
How Can I Convert Bam To Sam?
bam next-gen-sequencing sam
updated 8 months ago by 43k • written 13.9 years ago by 5.0k
143
votes
14
replies
169k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 6 months ago by 43k • written 14.1 years ago by 161k
147
votes
31
replies
138k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line fasta bash
updated 9 months ago by 43k • written 12.2 years ago by ★ 2.9k
68
votes
18
replies
131k
views
14 follow
from .BAM to .BAI using samtools
next-gen-sequencing samtools
updated 3 months ago by 161k • written 9.6 years ago by ▴ 870
77
votes
26
replies
121k
views
15 follow
How to count fastq reads
sequence next-gen fastq reads
updated 5 months ago by ★ 2.8k • written 9.1 years ago by ▴ 260
103
votes
34
replies
114k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 4 months ago by 43k • written 12.0 years ago by ▴ 390
105
votes
15
replies
113k
views
16 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 8 weeks ago by ▴ 140 • written 12.0 years ago by 12k
124
votes
56
replies
103k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 7 months ago by ▴ 30 • written 9.9 years ago by ▴ 370
171
votes
41
replies
98k
views
27 follow
Multiline Fasta To Single Line Fasta
fasta
updated 7 months ago by 43k • written 12.9 years ago by ▴ 250
105
votes
31
replies
95k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam picard samtools merge
updated 5 months ago by ▴ 450 • written 12.9 years ago by ★ 5.1k
97
votes
19
replies
94k
views
12 follow
How To Get The Sequence Of A Genomic Region From Ucsc?
ucsc fasta sequence
updated 7 months ago by 43k • written 14.2 years ago by 28k
103
votes
27
replies
89k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf tabix genome filter
updated 12 months ago by • 0 • written 12.0 years ago by ▴ 830
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
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
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
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
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
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
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene enrichment
updated 6 months ago by 43k • written 14.2 years ago by ★ 1.0k
164
votes
70
replies
61k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq next-gen-sequencing
updated 7 weeks ago by 43k • written 12.8 years ago by ★ 1.8k
93
votes
19
replies
60k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 11 months ago by 43k • written 13.7 years ago by ★ 2.6k
52
votes
8
replies
60k
views
7 follow
Subsampling Bam File With Samtools
bam samtools
updated 4 months ago by ▴ 10 • written 10.8 years ago by ▴ 250
17
votes
6
replies
59k
views
Turn Off Blast Search On Reverse Complement Strand In Blastn
blast sequence
updated 7 months ago by 43k • written 14.3 years ago by ★ 1.4k
45
votes
9
replies
59k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen RNA-Seq single-cell R
updated 9 months ago by ▴ 160 • written 4.5 years ago by ▴ 160
28
votes
22
replies
58k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r genomics entrez
updated 10 months ago by • 0 • written 11.1 years ago by ▴ 90
50
votes
13
replies
57k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 7 months ago by ▴ 160 • written 8.4 years ago by ▴ 490
61
votes
23
replies
57k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam mapping
updated 5 months ago by ★ 1.2k • written 11.2 years ago by ★ 1.3k
66
votes
19
replies
51k
views
17 follow
Tool To Find Out If Fastq Is In Sanger Or Phred64 Encoding?
fastq
updated 11 months ago by 43k • written 11.3 years ago by ★ 3.6k
68
votes
23
replies
49k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 8 weeks ago by • 0 • written 6.5 years ago by ★ 1.2k
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 10 months ago by 43k • written 12.1 years ago by ★ 1.5k
71
votes
15
replies
49k
views
10 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk minor major reference alleles
written 6.1 years ago by ▴ 420
3
votes
5
replies
48k
views
Convert text file to VCF file ?
vcf
updated 11 months ago by 43k • written 9.2 years ago by ▴ 280
34
votes
19
replies
47k
views
11 follow
Convert Refseq Id To Gene Name
refseq gene
updated 10 months ago by 43k • written 11.0 years ago by ▴ 250
9
votes
12
replies
46k
views
8 follow
Tools to view fastq file
fastq
updated 10 months ago by 43k • written 8.0 years ago by ▴ 40
35
votes
11
replies
45k
views
8 follow
Where Can I Download Some Bam Files?
bam RNA-seq
updated 4 months ago by 43k • written 12.0 years ago by ▴ 160
25
votes
9
replies
44k
views
Converting Gff To Bed With Bedtools?
gff bed bedtools
updated 3 months ago by 43k • written 11.3 years ago by ▴ 940
48
votes
9
replies
44k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 3 months ago by ▴ 640 • written 7.5 years ago by ▴ 570
35
votes
14
replies
44k
views
9 follow
How to filter vcf file on minimum genotype depth and quality for each sample
vcf bcftools
updated 7 months ago by ▴ 130 • written 7.9 years ago by ★ 5.3k
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation domain r
updated 8 months ago by 11k • written 11.3 years ago by ▴ 810
81
votes
21
replies
43k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed transcript ucsc biomart
updated 8 months ago by ▴ 210 • written 10.3 years ago by ▴ 750
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 18 days ago by ▴ 40 • written 6.8 years ago by ★ 1.3k
52
votes
14
replies
41k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 6 months ago by 161k • written 14.1 years ago by ▴ 660
6
votes
25
replies
39k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 11 months ago by • 0 • written 6.2 years ago by ▴ 130
23
votes
4
replies
39k
views
bcftools compressing and indexing vcf files
sequence bcftools vcf index
updated 6 months ago by 142k • written 5.7 years ago by ▴ 270
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 7 months ago by ▴ 70 • written 9.9 years ago by ▴ 170
19
votes
10
replies
38k
views
Ensembl ID to Gene Symbol
gene-symbol
updated 10 months ago by 43k • written 8.1 years ago by ▴ 330
13
votes
6
replies
37k
views
generating genome indexes with STAR
RNA-Seq STAR
updated 10 months ago by ★ 4.3k • written 7.9 years ago by ▴ 80
1,000 results • Page 1 of 20
Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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Recent Replies
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
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…
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