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334
votes
92
replies
240k
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
328
votes
54
replies
64k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 5 months ago by 43k • written 14.1 years ago by 24k
298
votes
122
replies
33k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 8 months ago by ▴ 290 • written 13.8 years ago by 11k
279
votes
29
replies
284k
views
25 follow
How To Filter Mapped Reads With Samtools
samtools
updated 17 months ago by 43k • written 11.5 years ago by ▴ 640
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 13.9 years ago by 5.0k
226
votes
39
replies
288k
views
33 follow
Gene Id Conversion Tool
david
updated 6 months ago by 43k • written 14.5 years ago by ▴ 620
208
votes
21
replies
180k
views
12 follow
Forward And Reverse Strand Conventions
sequence strand
updated 17 months ago by 100k • written 13.5 years ago by ★ 2.8k
188
votes
50
replies
73k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta sequence duplicates
updated 19 months ago by 43k • written 13.5 years ago by ▴ 340
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram visualization chromosome
updated 6 weeks ago by 54k • written 14.1 years ago by ★ 1.7k
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline general
updated 6 months ago by 43k • written 14.2 years ago by 28k
179
votes
51
replies
17k
views
26 follow
I Am Preparing A Course On Ngs: Any Suggestion ?
next-gen sequencing galaxy
updated 10.8 years ago by ▴ 600 • written 13.5 years ago by 161k
174
votes
30
replies
92k
views
17 follow
What Is The Best Method To Find Orthologous Genes Of A Species?
orthologues
updated 2.3 years ago by 43k • written 13.1 years ago by ▴ 620
172
votes
34
replies
26k
views
29 follow
Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r books bioconductor
updated 5 months ago by 43k • written 14.1 years ago by 54k
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
171
votes
26
replies
8.0k
views
12 follow
How Do You Acknowledge Biostar And Its Contributors In Your Research Output?
meta biostars
updated 14 months ago by 43k • written 13.2 years ago by 3.2k
166
votes
52
replies
129k
views
28 follow
Fastq Convert To Fasta
perl
10.5 years ago by biolab ★ 1.4k
164
votes
8
replies
180k
views
Generate vcf.gz file and its index file vcf.gz.tbi
vcf tabix
updated 22 months ago by 43k • written 11.4 years ago by ▴ 450
164
votes
70
replies
61k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq next-gen-sequencing
updated 5 weeks ago by 43k • written 12.8 years ago by ★ 1.8k
163
votes
64
replies
87k
views
39 follow
Selecting Random Pairs From Fastq?
random fastq illumina sequence
updated 3 months ago by 43k • written 13.1 years ago by 4.1k
160
votes
19
replies
40k
views
16 follow
Why Does Rna-Seq Read Count Fit Poisson Distribution?
rna-seq modeling
updated 2.4 years ago by 43k • written 10.5 years ago by ▴ 730
159
votes
24
replies
63k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing splicing rna-seq
updated 10 months ago by 43k • written 11.2 years ago by 11k
155
votes
44
replies
32k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 22 months ago by 43k • written 10.3 years ago by ★ 2.1k
154
votes
17
replies
30k
views
13 follow
What Are The Big Questions That Bioinformatics And Computational Biology Will Be Answering In The Next Few Years?
updated 22 months ago by 43k • written 12.3 years ago by 26k
153
votes
27
replies
11k
views
21 follow
The Best Question To Ask In A Bioinformatics Seminar
subjective
updated 13.3 years ago by ★ 1.1k • written 13.4 years ago by 28k
153
votes
32
replies
8.6k
views
23 follow
Picking A Programming Language And Where To Begin
programming next-gen sequencing c subjective
updated 12.3 years ago by ▴ 60 • written 12.8 years ago by ★ 2.8k
151
votes
42
replies
180k
views
22 follow
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
heatmap r
updated 23 months ago by 43k • written 12.2 years ago by 20k
147
votes
13
replies
25k
views
Alignment and mapping
alignment next-gen mapping
updated 8.2 years ago by 8.3k • written 8.2 years ago by ▴ 760
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
144
votes
14
replies
22k
views
15 follow
What Are The Classic Papers In Bioinformatics?
literature papers history
updated 3.1 years ago by 22k • written 13.5 years ago by 18k
143
votes
14
replies
169k
views
16 follow
What Is The Sequencing 'Depth' ?
next-gen sequencing
updated 5 months ago by 43k • written 14.1 years ago by 161k
143
votes
33
replies
30k
views
20 follow
C/C++ Libraries For Bioinformatics?
c c
updated 5.1 years ago by ▴ 50 • written 13.9 years ago by 13k
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 87k • written 6.5 years ago by ★ 1.9k
138
votes
33
replies
66k
views
19 follow
VCF files: Change Chromosome Notation
vcf next-gen sequence
updated 18 months ago by 43k • written 10.0 years ago by ▴ 490
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 19k
136
votes
26
replies
25k
views
14 follow
Best Way For A Beginner To Get Up To Speed On Unix Quickly?
unix perl genomics
updated 14 months ago by 43k • written 12.3 years ago by ▴ 300
136
votes
29
replies
7.6k
views
16 follow
How Do We Discourage Ad-Hoc Bioinformatic Analyses?
software
updated 2.0 years ago by 43k • written 13.4 years ago by 22k
135
votes
18
replies
170k
views
16 follow
Blast - Formatting Output
blast format output
updated 16 months ago by ▴ 30 • written 10.4 years ago by ▴ 320
134
votes
27
replies
45k
views
14 follow
Why Are There Many Rna-Seq Hits To Intronic Regions?
rna-seq
updated 2.0 years ago by 43k • written 12.1 years ago by 33k
131
votes
48
replies
16k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux subjective
updated 12.7 years ago by ★ 2.6k • written 12.7 years ago by 11k
131
votes
19
replies
183k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 3.0 years ago by • 0 • written 11.9 years ago by ▴ 370
130
votes
37
replies
14k
views
27 follow
What Are The Obsolete Research Topics In Bioinformatics?
updated 12.7 years ago by ★ 1.3k • written 12.7 years ago by ▴ 820
130
votes
19
replies
31k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq alignment next-gen R assembly
updated 3 months ago by 43k • written 4.6 years ago by ▴ 750
129
votes
32
replies
129k
views
29 follow
Is There A Free Alternative To Ingenuity Pathway Analysis?
network pathway
updated 2.1 years ago by 43k • written 13.2 years ago by ▴ 540
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
124
votes
29
replies
7.3k
views
18 follow
What License Do You Use When You Release Code And Data?
software general subjective
updated 5 months ago by 43k • written 14.1 years ago by 7.4k
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 13.8 years ago by 5.0k
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
122
votes
17
replies
76k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping genome
updated 2.1 years ago by 43k • written 13.0 years ago by ▴ 370
121
votes
29
replies
36k
views
11 follow
PCA in a RNA seq analysis
RNA-Seq pca
updated 5.4 years ago by 28k • written 6.5 years ago by ▴ 330
121
votes
7
replies
118k
views
Bam And Indexed Bam Files
bam index
12.3 years ago by Sahel ▴ 260
1,000 results • Page 1 of 20
Recent Votes
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
Answer: Design matrix Differential expression analysis
A: extract dendrogram cluster from pheatmap
extract dendrogram cluster from pheatmap
Answer: Searching for gene in multiple genomes
Comment: RNA velocity for smart-seq2 dataset
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Comment: Design matrix Differential expression analysis by SHN ▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx by vjanve • 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction by Expert ▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction by ATpoint 82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error by Ruqaiya • 0
This the tool still problematic?
Comment: Segmentation error while using a tool by Ruqaiya • 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool by Ruqaiya • 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool by Mensur Dlakic ★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool by Thanujay S • 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA by Thanujay S • 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool by Ruqaiya • 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2 by GenoMax 142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download by GenoMax 142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified. by GenoMax 142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis by Gordon Smyth ★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
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