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1,000 results • Page
2 of 20
Sort: Views
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Views
Votes
Replies
234
votes
176
replies
83k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 3 months ago by
Ram
38k • written 7.5 years ago by
TriS
★ 4.6k
83
votes
16
replies
82k
views
9 follow
Number of mapped reads from BAM file
bam
sam
reads
mapping
updated 11 weeks ago by
bhanu.chandra1
▴ 50 • written 7.8 years ago by
Prakki Rama
★ 2.6k
97
votes
31
replies
80k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 7 months ago by
Ram
38k • written 11.6 years ago by
2184687-1231-83-
★ 5.0k
79
votes
22
replies
80k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen
sequencing
fasta
rna
r
perl
updated 11 weeks ago by
Ram
38k • written 11.3 years ago by
Hamilton
▴ 290
106
votes
45
replies
79k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 5 months ago by
aswinssoman
▴ 20 • written 10.5 years ago by
Mchimich
▴ 320
70
votes
20
replies
79k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 4 weeks ago by
Ram
38k • written 12.2 years ago by
Unode
▴ 180
185
votes
43
replies
78k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 5 months ago by
Ram
38k • written 12.9 years ago by
Yuri
★ 1.6k
120
votes
8
replies
77k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi
ucsc
grch38
hg38
updated 13 months ago by
Ram
38k • written 8.4 years ago by
pwg46
▴ 520
55
votes
11
replies
77k
views
8 follow
merge large amount of fastq files into a single one
ChIP-Seq
fastq
updated 8 months ago by
Ram
38k • written 7.9 years ago by
catherine
▴ 220
33
votes
4
replies
76k
views
7 follow
Merging Bam Files
picard
samtools
updated 3.7 years ago by
abhijit.synl
▴ 60 • written 11.1 years ago by
Tryingtogetthere
▴ 180
99
votes
16
replies
75k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq
coverage
8.2 years ago by
Obi Griffith
20k
136
votes
25
replies
74k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 10 months ago by
Ram
38k • written 10.8 years ago by
Ying W
★ 4.2k
157
votes
62
replies
73k
views
37 follow
Selecting Random Pairs From Fastq?
random
fastq
sequence
illumina
code
updated 7 months ago by
erin.baschal
• 0 • written 11.9 years ago by
Ketil
4.1k
126
votes
24
replies
73k
views
18 follow
Sequence Length Distribution From A Fastq File
sequence
length
fastq
updated 3.8 years ago by
LuckyLuck
• 0 • written 9.7 years ago by
deepthithomaskannan
▴ 360
92
votes
24
replies
72k
views
19 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 12 months ago by
ashotmarg2004
▴ 120 • written 10.7 years ago by
Rubal7
▴ 820
15
votes
12
replies
71k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast
blastn
sift
makeblastdb
updated 6 months ago by
Luke
• 0 • written 8.3 years ago by
arronslacey
▴ 310
20
votes
2
replies
70k
views
Subsetting in R based on row name?
R
updated 6.8 years ago by
Devon Ryan
102k • written 6.8 years ago by
hakimelakhrass
▴ 80
103
votes
12
replies
70k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools
intersect
updated 3 months ago by
Ram
38k • written 11.3 years ago by
Bioscientist
★ 1.7k
43
votes
25
replies
70k
views
10 follow
Will A Masters In Bioinformatics Help Me In Getting A Job?
career
education
updated 11.9 years ago by
Eric Fournier
★ 1.4k • written 11.9 years ago by
Bioinfo
▴ 50
235
votes
45
replies
69k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen
sequencing
illumina
exome
human
updated 11.6 years ago by
User 9126
▴ 50 • written 12.7 years ago by
Biomed
4.8k
122
votes
17
replies
69k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping
genome
updated 11 months ago by
Ram
38k • written 11.8 years ago by
Nick
▴ 370
33
votes
17
replies
69k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray
heatmap
updated 20 days ago by
Ram
38k • written 11.7 years ago by
Fahmida
▴ 80
67
votes
18
replies
68k
views
17 follow
Project For A Beginner Bioinformatics Student
project
java
updated 7 months ago by
Ram
38k • written 11.2 years ago by
And
▴ 230
77
votes
19
replies
68k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools
bcftools
htslib
Tutorial
updated 16 days ago by
jcurry01
• 0 • written 4.5 years ago by
otwtgin2010
▴ 530
40
votes
14
replies
68k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 9 months ago by
Ram
38k • written 12.1 years ago by
Elena
▴ 250
22
votes
2
replies
68k
views
How Can I Make A Bed File?
bed
updated 11.4 years ago by
John M
▴ 260 • written 11.4 years ago by
Omid
▴ 580
194
votes
44
replies
67k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 4 weeks ago by
Ram
38k • written 10.4 years ago by
Obi Griffith
20k
24
votes
23
replies
67k
views
7 follow
Multiple Histograms In One Plot
r
updated 14 months ago by
Ram
38k • written 9.6 years ago by
Assa Yeroslaviz
★ 1.8k
188
votes
50
replies
67k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 4 months ago by
Ram
38k • written 12.3 years ago by
Zhangleisdau
▴ 340
138
votes
21
replies
67k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer
gene
database
oncogene
tumor
2.3 years ago by
Malachi Griffith
19k
1
vote
2
replies
66k
views
"SyntaxError: unexpected EOF while parsing " IN PYTHON 3.7
PYTHON
updated 22 months ago by
Istvan Albert
96k • written 2.8 years ago by
geethus2009
• 0
59
votes
15
replies
66k
views
9 follow
BAM/SAM to FASTA conversion
sam
bam
updated 10 months ago by
Ram
38k • written 8.0 years ago by
biolab
★ 1.4k
74
votes
13
replies
65k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 3 months ago by
Ram
38k • written 9.2 years ago by
Nicholas Spies
★ 1.2k
40
votes
15
replies
64k
views
14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix
conversion
entrez
updated 4 months ago by
Ram
38k • written 9.6 years ago by
Josh
▴ 140
111
votes
25
replies
64k
views
14 follow
Is My Bam File Sorted ?
bam
next-gen
sequencing
sort
updated 1 day ago by
Miguel
▴ 10 • written 12.0 years ago by
Pierre Lindenbaum
152k
19
votes
8
replies
63k
views
6 follow
Pheatmap Annotation
r
heatmap
updated 7.5 years ago by
wm
▴ 550 • written 9.9 years ago by
James
▴ 80
51
votes
18
replies
63k
views
10 follow
Extract User Defined Region From An Fasta File
sequence
fasta
updated 5.5 years ago by
tuomastik
▴ 30 • written 11.6 years ago by
Palu
▴ 290
35
votes
9
replies
63k
views
8 follow
Minor allele frequency calculation
SNP
next-gen
updated 8 months ago by
Ram
38k • written 8.2 years ago by
Tark
▴ 50
20
votes
15
replies
62k
views
12 follow
Python Script To Translate Rna Sequences To Protein Sequences
python
biopython
translation
updated 9.4 years ago by
viv_bio
▴ 50 • written 12.3 years ago by
Studentguy
▴ 70
40
votes
7
replies
62k
views
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
r
rna
heatmap
clustering
gene
updated 7 months ago by
Ram
38k • written 11.3 years ago by
Kanne
▴ 450
51
votes
15
replies
62k
views
15 follow
Any Recommendations For Software For Drawing Plasmid Maps?
visualization
software
updated 9 months ago by
Ram
38k • written 11.7 years ago by
Michael Petronio
▴ 70
48
votes
13
replies
61k
views
9 follow
Sequence Number Count In Fastq.Gz File
counts
sequence
fastq
updated 13 months ago by
Ram
38k • written 11.6 years ago by
Bioscientist
★ 1.7k
25
votes
5
replies
61k
views
7 follow
Rpkm Calculation For Genes
rpkm
rna-seq
updated 10.3 years ago by
JC
13k • written 10.3 years ago by
siddharth.sethi5
▴ 270
53
votes
4
replies
60k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence
next-gen-sequencing
updated 3 months ago by
Ram
38k • written 8.2 years ago by
mangfu100
▴ 780
53
votes
10
replies
60k
views
6 follow
Fold change - a final explanation
RNA-Seq
updated 2.4 years ago by
naloy
• 0 • written 4.3 years ago by
Sebastian Hesse
▴ 320
36
votes
14
replies
59k
views
9 follow
What Is The Difference Between Hg18 And Hg19?
genome
hg
hg
updated 11.0 years ago by
Jorge Amigo
14k • written 11.0 years ago by
Sara
▴ 170
102
votes
30
replies
59k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
tool
updated 7 months ago by
Ram
38k • written 12.9 years ago by
Biostar User
★ 1.0k
152
votes
24
replies
59k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
splicing
tools
rna-seq
alternative-splicing
updated 7 months ago by
Ram
38k • written 9.9 years ago by
Nicolas Rosewick
10k
2
votes
10
replies
58k
views
R: remove rows by a list of rownames
R
updated 9 months ago by
Ram
38k • written 8.0 years ago by
silvi_free88
▴ 50
17
votes
6
replies
58k
views
Turn Off Blast Search On Reverse Complement Strand In Blastn
sequence
blast
updated 2.5 years ago by
yasopi9568
• 0 • written 13.0 years ago by
Zhaorong
★ 1.4k
1,000 results • Page
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Recent Votes
Answer: Using Entrez Utilities to query the Nucleotide database by collection_date
Comment: Subbmission Data
Comment: Subbmission Data
Answer: Subbmission Data
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Comment: Bacterial metatranscriptomics with DESEQ2?
C: How to extend contigs from single-end reads?
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Comment: Subbmission Data
by
seidel
10k
GEO allows you to keep your data private for up to three years, AND has a mechanism where you can share it with reviewers without it being …
Comment: PyMOL: Gaps in protein structure yet shown by the sequence
by
spence.lank
▴ 10
The PDB ID for this structure is 7DK3 and the literature is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7775788/
Comment: Problem with tximport and plasmodium falciparum
by
ATpoint
69k
You do not do what I suggested above.
Comment: Relative frequencies of the nucleotides in Fasta files
by
xiaoleiusc
▴ 110
Hi, Hugo, I acknowledged you in my paper recently published. Thanks for your help! Xiao PS, paper link https://elifesciences.org/articles/8…
Comment: Stringtie prepDE.py script
by
Buffo
★ 2.0k
from the manual: -i a folder containing all sample sub-directories, or a text file with sample ID and path to its GTF file on each lin…
Comment: Using Entrez Utilities to query the Nucleotide database by collection_date
by
anomalous.lexeme
• 0
That looks pretty useful. I'll give that a try as well. Thank you very kindly for the help.
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
Juke34
7.5k
This script does not exist anymore in recent releases. Without any example I cannot help.
Comment: Create de novo repeat library
by
evoecogen
▴ 20
Are there any alternatives to ProtExcluder? I suddenly started to have problems with v1.2: The files blastx.out.fnolowm50seqm and blastx.o…
Comment: Find corresponding branch from gene tree in species tree
by
Charlotte West
▴ 40
Following your suggestion I've been playing around with Notung and seems like its got a lot of great features. I ran: ``` java -jar notung …
Comment: how to get an average ROC curve after 10-fold cross validation in r
by
Lisa
• 0
thanks for your help
Comment: docker build Command Works Yet It Does Not Create A Docker Container
by
Indira
• 0
So - I am trying to get around proxy issues but essentially installing required packages in a docker/sif then trying to use that to run an …
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
Ram
38k
Do not add answers unless you're **answering** the top level question. Use `Add Comment` or `Add Reply` instead as appropriate. I've moved …
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
BioinfoBee
• 0
@juke34 I tried the agat_sp_gxf_to_gff3.pl to sort the gff3 by their chromosome order but doesn't seems to work. Any suggestions?.
Comment: CNV Prediction Tools
by
Quentin M
▴ 60
Give a try to [CODEX2][1] [1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1578-y
Comment: Problem with tximport and plasmodium falciparum
by
bioinfo
▴ 20
Thank you. It does not seem to be that. I changed my script a bit. Now it looks like shown below: mart <- biomaRt::useMart("protists_…
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