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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
298
votes
122
replies
33k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 8 months ago by
jena
▴ 290 • written 13.8 years ago by
Eric Normandeau
11k
62
votes
95
replies
20k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA
CNV
genes
updated 15 months ago by
Di
▴ 10 • written 6.0 years ago by
Chaimaa
▴ 260
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
kalavattam
▴ 190 • written 13.3 years ago by
Biomed
5.0k
105
votes
81
replies
32k
views
17 follow
Duplicates on Illumina
duplicates
illumina
updated 20 months ago by
GenoMax
142k • written 7.3 years ago by
predeus
★ 2.0k
118
votes
74
replies
46k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 18 months ago by
GenoMax
142k • written 13.4 years ago by
Casbon
★ 3.3k
56
votes
72
replies
6.3k
views
8 follow
Dear biostars I really need your kindly help, please save me from this hardship situation
software error
mirddep2
perl
miRNAs
RNA-Seq
updated 7.5 years ago by
Nestor Wendt
▴ 100 • written 7.6 years ago by
zizigolu
★ 4.3k
105
votes
72
replies
18k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code
fasta
sequence
codegolf
updated 5.6 years ago by
zx8754
11k • written 13.8 years ago by
Eric Normandeau
11k
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
Ram
43k • written 12.8 years ago by
Panos
★ 1.8k
163
votes
64
replies
87k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 3 months ago by
Ram
43k • written 13.1 years ago by
Ketil
4.1k
38
votes
63
replies
20k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly
miseq
illumina
genome
updated 15 months ago by
Ram
43k • written 11.2 years ago by
Leszek
4.2k
34
votes
62
replies
6.4k
views
6 follow
Extract some features from a combined gene bank file in bash
gene
sequence
genome
gene bank
NCBI
updated 7.5 years ago by
Ram
43k • written 7.5 years ago by
zizigolu
★ 4.3k
117
votes
59
replies
33k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware
next-gen
updated 15 months ago by
Ram
43k • written 9.0 years ago by
Angelo Victoria
▴ 30
26
votes
57
replies
8.4k
views
how to generate CNV plot from VEP results
copy number alteration
VEP
CNV plot
updated 3.3 years ago by
Ram
43k • written 5.6 years ago by
nazaninhoseinkhan
▴ 520
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
William
▴ 30 • written 9.9 years ago by
kay
▴ 370
112
votes
56
replies
44k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq
next-gen
sequencing
fusion
updated 19 months ago by
Ram
43k • written 11.9 years ago by
KS
▴ 380
41
votes
55
replies
12k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
8.1 years ago by
midox
▴ 290
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
Ram
43k • written 14.1 years ago by
brentp
24k
46
votes
54
replies
7.1k
views
12 follow
fasta seq header
sequence
fasta
updated 7.2 years ago by
Matt Shirley
10k • written 7.2 years ago by
####
▴ 220
55
votes
53
replies
7.2k
views
How to determine species of paired-end .fastq files (low mapping rates and inconsistent findings)
bacteria
kraken
spades
blast
sendsketch
updated 4.4 years ago by
jbnrodriguez
▴ 30 • written 4.6 years ago by
LRStar
▴ 200
6
votes
53
replies
4.1k
views
how to download all sequences from web link
bash
linux
4.8 years ago by
Bioinfonext
▴ 460
166
votes
52
replies
129k
views
28 follow
Fastq Convert To Fasta
perl
10.5 years ago by
biolab
★ 1.4k
32
votes
51
replies
20k
views
8 follow
Getting Unmapped Reads: Comparing Fastq To Bam
fastq
samtools
bedtools
bam
updated 12.4 years ago by
brentp
24k • written 12.4 years ago by
User 9996
▴ 840
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
sarahhunter
▴ 600 • written 13.5 years ago by
Pierre Lindenbaum
161k
27
votes
50
replies
18k
views
7 follow
Extract fasta sequences from a large file using a list of names
fasta
updated 15 months ago by
Ram
43k • written 9.0 years ago by
fhsantanna
▴ 620
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
Ram
43k • written 13.5 years ago by
Zhangleisdau
▴ 340
94
votes
50
replies
53k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq
pca
updated 2.5 years ago by
BioNovice247
▴ 20 • written 6.5 years ago by
rachel.kubik12
▴ 220
22
votes
50
replies
17k
views
Why I can not install anything on R?
R
software error
5.6 years ago by
Za
▴ 140
12
votes
50
replies
4.2k
views
How can I find out the Linux version and what is the ftp command to install R and R Studio on Linux server?
R
7.2 years ago by
thomas.f.hahn2
▴ 100
85
votes
49
replies
10k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective
general
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Jarretinha
3.4k
72
votes
48
replies
8.5k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 14 months ago by
Ram
43k • written 13.1 years ago by
User 59
13k
39
votes
48
replies
7.0k
views
CUTADAPT in windows
sequencing
updated 15 months ago by
Ram
43k • written 9.0 years ago by
zizigolu
★ 4.3k
131
votes
48
replies
16k
views
19 follow
Justifying Learning Linux For Bioinformatics
linux
subjective
updated 12.7 years ago by
Guangchuang Yu
★ 2.6k • written 12.7 years ago by
Eric Normandeau
11k
22
votes
47
replies
5.3k
views
(solved) I couldn't reproduce the problem of max_target_seqs
blast
updated 5.1 years ago by
gb
★ 2.2k • written 5.6 years ago by
fishgolden
▴ 510
23
votes
47
replies
7.1k
views
6 follow
Dbsnp Individual Genotyping Information For Specific Snps
dbsnp
updated 13.1 years ago by
Khader Shameer
18k • written 13.1 years ago by
Andrea_Bio
★ 2.8k
18
votes
47
replies
4.7k
views
Fastq Trimmer by pattern
fastq
trimming
reads
terminal
7.2 years ago by
dzisis1986
▴ 70
37
votes
46
replies
6.9k
views
12 follow
Quick Programming Challenge: How Do I Calculate Reference Coverage From A Table Of Alignment Starts And Ends?
code
alignment
programming
updated 5.7 years ago by
Ram
43k • written 14.0 years ago by
Jeremy Leipzig
22k
92
votes
46
replies
12k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming
subjective
updated 14 months ago by
Ram
43k • written 12.8 years ago by
Andra Waagmeester
3.2k
43
votes
46
replies
4.3k
views
taking sequences of a list of miRNAs
miRNA
mirbase
sequence
gene
updated 7.6 years ago by
Ram
43k • written 7.6 years ago by
zizigolu
★ 4.3k
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
User 9126
▴ 50 • written 13.9 years ago by
Biomed
5.0k
108
votes
45
replies
86k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 20 months ago by
aswinssoman
▴ 70 • written 11.8 years ago by
Mchimich
▴ 320
4
votes
45
replies
7.8k
views
SAM file wrong? help with validatesamfile
EXOME
updated 13 months ago by
Ram
43k • written 7.9 years ago by
cristina_sabiers
▴ 110
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
22
votes
45
replies
13k
views
9 follow
Tool to separate human and mouse rna seq reads
RNA-Seq
next-gen-sequencing
updated 15 months ago by
Ram
43k • written 9.0 years ago by
Ron
★ 1.2k
155
votes
44
replies
32k
views
29 follow
Which Bioinformatic Friendly Pipeline Building Framework?
scripting
updated 22 months ago by
Ram
43k • written 10.3 years ago by
Carlos Borroto
★ 2.1k
185
votes
44
replies
83k
views
30 follow
Drawing Chromosome Ideograms With Data
ideogram
visualization
chromosome
updated 6 weeks ago by
Michael
54k • written 14.1 years ago by
Yuri
★ 1.7k
46
votes
44
replies
25k
views
9 follow
bash loop for alignment RNA-seq data
RNA-Seq
next-gen
alignment
updated 19 months ago by
Ram
43k • written 10.1 years ago by
Paul
★ 1.5k
121
votes
44
replies
21k
views
21 follow
What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
subjective
updated 14 months ago by
Ram
43k • written 13.9 years ago by
Madelaine Gogol
5.3k
99
votes
44
replies
24k
views
33 follow
Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
text
r
perl
python
updated 6.7 years ago by
grant.hovhannisyan
★ 2.6k • written 12.2 years ago by
John
★ 1.5k
90
votes
44
replies
60k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 2.0 years ago by
Ram
43k • written 13.0 years ago by
Ryan D
★ 3.4k
43
votes
44
replies
5.9k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics
amplicon
macbook
Intel
MacOs
updated 6 months ago by
steve
★ 3.5k • written 7 months ago by
l.gallucci
▴ 10
1,000 results • Page
1 of 20
Recent Votes
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
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
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Recent Replies
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 20
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 20
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
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…
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