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1,000 results • Page
2 of 20
Sort: Views
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Views
Votes
Replies
238
votes
176
replies
88k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 4 months ago by
Ram
40k • written 8.2 years ago by
TriS
★ 4.7k
105
votes
31
replies
88k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 14 months ago by
Ram
40k • written 12.2 years ago by
2184687-1231-83-
★ 5.1k
79
votes
22
replies
86k
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 10 months ago by
Ram
40k • written 12.0 years ago by
Hamilton
▴ 290
43
votes
15
replies
86k
views
9 follow
How Do I Count The Number Values Less Than X In A Column Using R ?
rna
edger
r
counts
updated 8.9 years ago by
seidel
11k • written 12.5 years ago by
Jason
▴ 920
56
votes
11
replies
86k
views
8 follow
merge large amount of fastq files into a single one
ChIP-Seq
fastq
updated 16 months ago by
Ram
40k • written 8.5 years ago by
catherine
▴ 250
72
votes
20
replies
84k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl
identifiers
mapping
updated 8 months ago by
Ram
40k • written 12.9 years ago by
Unode
▴ 180
108
votes
45
replies
83k
views
30 follow
How To Extract A Sequence From A Big (6Gb) Multifasta File ?
fasta
updated 13 months ago by
aswinssoman
▴ 40 • written 11.2 years ago by
Mchimich
▴ 320
97
votes
27
replies
82k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 4 months ago by
NIRJHAR
• 0 • written 11.3 years ago by
Rubal7
▴ 820
185
votes
43
replies
80k
views
29 follow
Drawing Chromosome Ideograms With Data
chromosome
visualization
ideogram
updated 12 months ago by
Ram
40k • written 13.5 years ago by
Yuri
★ 1.6k
86
votes
22
replies
80k
views
14 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 11 weeks ago by
sifa.khan
• 0 • written 5.2 years ago by
otwtgin2010
▴ 580
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 11 days ago by
rohitsatyam102
▴ 750 • written 12.5 years ago by
Ketil
4.1k
137
votes
25
replies
80k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 18 months ago by
Ram
40k • written 11.4 years ago by
Ying W
★ 4.2k
128
votes
24
replies
80k
views
18 follow
Sequence Length Distribution From A Fastq File
sequence
length
fastq
updated 4.4 years ago by
LuckyLuck
• 0 • written 10.4 years ago by
deepthithomaskannan
▴ 370
17
votes
12
replies
79k
views
8 follow
BLAST Database error: No alias or index file found for nucleotide database
blast
blastn
sift
makeblastdb
updated 13 months ago by
Luke
• 0 • written 8.9 years ago by
arronslacey
▴ 320
120
votes
8
replies
79k
views
GRCh37/38(NCBI) vs hg19/hg38(UCSC)
ncbi
ucsc
grch38
hg38
updated 21 months ago by
Ram
40k • written 9.0 years ago by
pwg46
▴ 520
33
votes
4
replies
78k
views
7 follow
Merging Bam Files
picard
samtools
updated 4.4 years ago by
abhijit.synl
▴ 60 • written 11.7 years ago by
Tryingtogetthere
▴ 180
60
votes
10
replies
77k
views
6 follow
Fold change - a final explanation
RNA-Seq
updated 3.1 years ago by
naloy
▴ 10 • written 5.0 years ago by
Sebastian Hesse
▴ 340
99
votes
16
replies
76k
views
15 follow
How Much Coverage Do We Need For An Rna-Seq Experiment?
rna-seq
coverage
8.8 years ago by
Obi Griffith
20k
104
votes
12
replies
76k
views
7 follow
Bedtools Compare Multiple Bed Files?
bedtools
intersect
updated 11 months ago by
Ram
40k • written 11.9 years ago by
Bioscientist
★ 1.7k
50
votes
14
replies
75k
views
10 follow
Tutorial:
Using R in Conda
R
updated 6 months ago by
Ram
40k • written 3.2 years ago by
rohitsatyam102
▴ 750
22
votes
2
replies
73k
views
How Can I Make A Bed File?
bed
updated 12.1 years ago by
John M
▴ 260 • written 12.1 years ago by
Omid
▴ 580
20
votes
2
replies
73k
views
Subsetting in R based on row name?
R
updated 7.5 years ago by
Devon Ryan
103k • written 7.5 years ago by
hakimelakhrass
▴ 80
122
votes
17
replies
72k
views
8 follow
What Are Phased And Unphased Genotypes?
genotyping
genome
updated 18 months ago by
Ram
40k • written 12.4 years ago by
Nick
▴ 370
59
votes
15
replies
72k
views
9 follow
BAM/SAM to FASTA conversion
sam
bam
updated 17 months ago by
Ram
40k • written 8.7 years ago by
biolab
★ 1.4k
43
votes
25
replies
71k
views
10 follow
Will A Masters In Bioinformatics Help Me In Getting A Job?
career
education
updated 12.5 years ago by
Eric Fournier
★ 1.4k • written 12.5 years ago by
Bioinfo
▴ 50
67
votes
18
replies
71k
views
17 follow
Project For A Beginner Bioinformatics Student
project
java
updated 14 months ago by
Ram
40k • written 11.9 years ago by
And
▴ 230
235
votes
45
replies
70k
views
34 follow
What Is The Best Pipeline For Human Whole Exome Sequencing?
next-gen
sequencing
illumina
exome
human
updated 12.3 years ago by
User 9126
▴ 50 • written 13.3 years ago by
Biomed
4.9k
188
votes
50
replies
70k
views
41 follow
How To Remove The Same Sequences In The Fasta Files?
fasta
sequence
duplicates
updated 12 months ago by
Ram
40k • written 13.0 years ago by
Zhangleisdau
▴ 340
27
votes
10
replies
70k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 6 months ago by
Ram
40k • written 2.5 years ago by
Nitin Narwade
★ 1.4k
42
votes
14
replies
70k
views
9 follow
Synonymous And Non-Synonymous Snps
snp
updated 17 months ago by
Ram
40k • written 12.7 years ago by
Elena
▴ 250
33
votes
17
replies
70k
views
14 follow
How To Draw A Heat Map For Gene Expression Data?
microarray
heatmap
updated 8 months ago by
Ram
40k • written 12.3 years ago by
Fahmida
▴ 80
196
votes
44
replies
70k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 8 months ago by
Ram
40k • written 11.0 years ago by
Obi Griffith
20k
138
votes
21
replies
69k
views
18 follow
Database Of Tumor Suppressors And/Or Oncogenes
cancer
gene
database
oncogene
tumor
3.0 years ago by
Malachi Griffith
19k
51
votes
18
replies
69k
views
10 follow
Extract User Defined Region From An Fasta File
sequence
fasta
updated 6.2 years ago by
tuomastik
▴ 30 • written 12.2 years ago by
Palu
▴ 290
19
votes
8
replies
68k
views
6 follow
Pheatmap Annotation
r
heatmap
updated 8.1 years ago by
wm
▴ 550 • written 10.6 years ago by
James
▴ 80
24
votes
23
replies
68k
views
7 follow
Multiple Histograms In One Plot
r
updated 22 months ago by
Ram
40k • written 10.3 years ago by
Assa Yeroslaviz
★ 1.8k
40
votes
15
replies
67k
views
14 follow
Converting Affymetrix Probes To Gene Ids
affymetrix
conversion
entrez
updated 12 months ago by
Ram
40k • written 10.2 years ago by
Josh
▴ 140
115
votes
25
replies
67k
views
14 follow
Is My Bam File Sorted ?
bam
next-gen
sequencing
sort
updated 7 months ago by
Miguel
▴ 10 • written 12.7 years ago by
Pierre Lindenbaum
157k
1
vote
2
replies
67k
views
"SyntaxError: unexpected EOF while parsing " IN PYTHON 3.7
PYTHON
updated 2.5 years ago by
Istvan Albert
98k • written 3.4 years ago by
geethus2009
• 0
35
votes
9
replies
66k
views
8 follow
Minor allele frequency calculation
SNP
next-gen
updated 16 months ago by
Ram
40k • written 8.9 years ago by
Tark
▴ 50
75
votes
13
replies
66k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 11 months ago by
Ram
40k • written 9.9 years ago by
Nicholas Spies
★ 1.2k
20
votes
15
replies
66k
views
12 follow
Python Script To Translate Rna Sequences To Protein Sequences
python
biopython
translation
updated 10.1 years ago by
viv_bio
▴ 50 • written 13.0 years ago by
Studentguy
▴ 70
56
votes
4
replies
66k
views
What is difference between soft-clipped and hard-clipped in SAM specification?
sequence
next-gen-sequencing
updated 11 months ago by
Ram
40k • written 8.9 years ago by
mangfu100
▴ 800
51
votes
15
replies
65k
views
15 follow
Any Recommendations For Software For Drawing Plasmid Maps?
visualization
software
updated 17 months ago by
Ram
40k • written 12.3 years ago by
Michael Petronio
▴ 70
50
votes
15
replies
65k
views
12 follow
Sequence Number Count In Fastq.Gz File
counts
sequence
fastq
updated 7 months ago by
Ram
40k • written 12.3 years ago by
Bioscientist
★ 1.7k
361
votes
58
replies
64k
views
44 follow
Forum:
Recommend Your Favorite Bioinformatics Books
books
education
written 13.6 years ago by
Istvan Albert
98k
50
votes
17
replies
64k
views
11 follow
Extract fasta sequences from a file using a list in another file.
fasta
header
extract
awk
grep
updated 2.7 years ago by
Rashedul Islam
▴ 470 • written 5.3 years ago by
EBP91
▴ 50
11
votes
9
replies
64k
views
7 follow
combining fasta files
windows
fasta
notepad
updated 10 months ago by
Devarakonda
• 0 • written 8.7 years ago by
vigneshprbh37
▴ 30
92
votes
18
replies
64k
views
12 follow
Sequence length from Fasta
fasta
updated 9 months ago by
Ram
40k • written 8.9 years ago by
bongbang
▴ 80
9
votes
6
replies
63k
views
How To Calculate Coverage
fastq
coverage
updated 9.7 years ago by
r.follador
▴ 90 • written 9.7 years ago by
HG
★ 1.2k
1,000 results • Page
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Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Recent Replies
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again...
by
GenoMax
134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files
by
Alex Reynolds
35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
• 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
• 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File
by
Reem
• 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR
by
Trivas
★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output
by
langziv
▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
by
Pierre Lindenbaum
157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
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