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1,000 results • Page
6 of 20
Sort: replies
Rank
Views
Votes
Replies
7
votes
17
replies
8.2k
views
10 follow
Python FASTA scripting
Python
FASTA
updated 11 months ago by
Ram
43k • written 4.6 years ago by
damonlbp
▴ 20
27
votes
17
replies
22k
views
8 follow
BioPython: convert fasta to fastq without quality score input file
parsing
phred
fasta
BioPython
fastq
updated 11 months ago by
capemaster
• 0 • written 10.0 years ago by
Josh Herr
5.8k
14
votes
17
replies
19k
views
6 follow
HISAT2 command help
RNA-Seq
alignment
updated 4 months ago by
DareDevil
★ 4.3k • written 8.3 years ago by
dina.hesham139
▴ 170
8
votes
17
replies
1.9k
views
7 follow
How to limit fasta header to 40 characters?
unix
seqkit
fasta
updated 8 months ago by
Roop
• 0 • written 8 months ago by
fishingline37
• 0
6
votes
17
replies
1.7k
views
Filtering rows based on a list if all the entries of the list correspond to a specific row value
row-matching
sorting
filtering
updated 11 months ago by
Ram
43k • written 12 months ago by
bionix
▴ 10
10
votes
17
replies
1.9k
views
Building reference dbSNP file using WGS samples
NGS
WGS
Variant-calling
non-model
Bootstrapping
5 months ago by
analyst
▴ 50
0
votes
17
replies
1.2k
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
4 months ago by
Foad
▴ 10
9
votes
17
replies
2.6k
views
Interpret plots from DiffBind
DiffBind
updated 9 months ago by
Rory Stark
★ 2.0k • written 11 months ago by
Chris
▴ 280
28
votes
17
replies
5.1k
views
7 follow
Tool:
PCAtools: everything Principal Components Analysis
eigenvector
pca
bioconductor
R
updated 11 months ago by
Ram
43k • written 5.3 years ago by
Kevin Blighe
88k
17
votes
17
replies
2.0k
views
6 follow
Forum:
Journal for beginners
journal
updated 11 months ago by
Ram
43k • written 6.1 years ago by
heref
▴ 20
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 27 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
0
votes
17
replies
3.0k
views
Processing Fast5 files from ONT for direct RNA
Nanopore
Nanopolish
ELIGOS2
Fast5
Tombo
updated 10 months ago by
kenneditodd
▴ 50 • written 17 months ago by
Shagnik
• 0
28
votes
16
replies
31k
views
11 follow
How Do I Convert From Bed Format To Gff Format?
gff
galaxy
bed
updated 7 months ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 10 months ago by
Ram
43k • written 4.3 years ago by
Ankit
▴ 500
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
43k • written 5.2 years ago by
Star
▴ 60
8
votes
16
replies
5.3k
views
9 follow
visualize CNV data based on WGS
CNV
updated 7 weeks ago by
clealk
▴ 50 • written 6.3 years ago by
Bogdan
★ 1.4k
50
votes
16
replies
14k
views
12 follow
Tool:
Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr
software
ngs
updated 11 months ago by
Ram
43k • written 10.6 years ago by
arnaud.desfeux
▴ 450
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 7 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
3
votes
16
replies
2.7k
views
design matrix for dge
limma
differential-gene-expression
r
updated 5 weeks ago by
Ram
43k • written 8.0 years ago by
1234anjalianjali1234
▴ 50
0
votes
16
replies
1.1k
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
4 weeks ago by
biwdpang
• 0
5
votes
16
replies
2.0k
views
MEME calling motifs from eCLIP-seq file generate no information
software-error
RNA-Seq
next-gen
ChIP-Seq
updated 11 months ago by
Ram
43k • written 4.1 years ago by
Kai_Qi
▴ 130
18
votes
16
replies
1.8k
views
Forum:
Why are people not working on gene prioritization and candidate gene selection for new experiment design?
gene-prioritization
updated 11 months ago by
Ram
43k • written 5.6 years ago by
prasadhendre
▴ 20
7
votes
16
replies
905
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
15 days ago by
Ruqaiya
• 0
17
votes
16
replies
14k
views
10 follow
How to extract the longest isoform from multi fasta file
perl
extract
fasta
python
isoform
updated 5 weeks ago by
Madeleine
• 0 • written 9.8 years ago by
jon.brate
▴ 310
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 8 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
16
votes
16
replies
7.7k
views
6 follow
Tool:
Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data
annotation
fusion
rna-seq
ngs
updated 10 months ago by
Ram
43k • written 10.7 years ago by
mikhail.shugay
3.5k
26
votes
16
replies
6.7k
views
Which Human Tumor Cell Line/Sample Genomes Have Been Already Sequenced Completely?
genome
next-gen-sequencing
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Fred Fleche
4.3k
3
votes
16
replies
1.8k
views
Simulate reads for positions in a vcf file
variant-calling
simulation
bam
vcf
updated 6 months ago by
Brian Bushnell
20k • written 10 months ago by
berndmann
▴ 10
15
votes
16
replies
4.8k
views
Gene Expression Experiment Using Ngs Data
next-gen-sequencing
gene-expression
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Eric Normandeau
11k
11
votes
16
replies
8.0k
views
6 follow
Frequency of a unique sequence in a fasta file
sequencing
FASTA
updated 9 months ago by
Shashi
• 0 • written 9.2 years ago by
Tanvir Ahamed
▴ 350
0
votes
16
replies
3.9k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 11 months ago by
Ram
43k • written 5.9 years ago by
rororo
▴ 10
16
votes
16
replies
5.6k
views
how to run a tool (package) installed into anaconda environment ..using mac terminal
genome
updated 11 months ago by
Ram
43k • written 4.0 years ago by
Pegasus
▴ 100
8
votes
16
replies
2.9k
views
Tool:
CuteVcf : A Qt application to view VCF file
htslib
gui
vcf
tabix
Qt
updated 10 months ago by
Ram
43k • written 7.4 years ago by
sacha
★ 2.4k
36
votes
16
replies
14k
views
8 follow
How to identify 16s sequences from binning data(contigs)?
genome
Assembly
sequence
blast
updated 10 months ago by
Kermit
▴ 90 • written 8.6 years ago by
liuyifan2014
▴ 110
6
votes
16
replies
2.9k
views
Tool:
MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
RNA-Seq
ChIP-Seq
updated 10 months ago by
Ram
43k • written 7.6 years ago by
Bohdan Khomtchouk
▴ 350
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 25 days ago by
Hagen
▴ 10 • written 10.3 years ago by
filipzembol
▴ 180
12
votes
16
replies
11k
views
8 follow
fpkm to tpm conversion
R
next-gen
updated 3 months ago by
DareDevil
★ 4.3k • written 6.7 years ago by
sayamsmruti
▴ 20
9
votes
16
replies
2.3k
views
Can't liftover vcf file from hg19 to hg38
bcftools
updated 10 months ago by
Ram
43k • written 15 months ago by
Victor
▴ 10
4
votes
16
replies
1.0k
views
hisat2 location does not exist
hisat2
updated 11 weeks ago by
Ram
43k • written 12 weeks ago by
Eric
• 0
42
votes
16
replies
34k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 7 months ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
chparada
▴ 70
6
votes
16
replies
2.2k
views
samtools collate
samtools
10 months ago by
Sara
▴ 30
74
votes
16
replies
4.8k
views
10 follow
Tools & Techniques Bioinformatician Have To Master?
subjective
updated 10 months ago by
Ram
43k • written 13.2 years ago by
Thaman
★ 3.3k
30
votes
16
replies
2.3k
views
9 follow
Forum:
Which programming langauge shall I start as a beginner in Bioinformatics
programming-language
single-cell
updated 11 months ago by
Ram
43k • written 4.1 years ago by
nkg.bb
• 0
2
votes
16
replies
6.3k
views
Converting Microarray SNP data into VCF format
Affymetrix
SNP
VCF
RNA-Seq
Microarray
updated 12 months ago by
Xu
• 0 • written 5.4 years ago by
Susmita Mandal
▴ 110
20
votes
16
replies
20k
views
6 follow
Conversion of Gene Name to Ensembl ID
gene
RNA-Seq
R
genome
updated 6 months ago by
Nat.Nataren
▴ 10 • written 4.1 years ago by
bazok
▴ 20
4
votes
16
replies
1.9k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
updated 11 weeks ago by
Ram
43k • written 7 months ago by
ella
• 0
16
votes
16
replies
2.3k
views
Species identifcation using 16s rRNA
16srRNA
fasta
updated 7 months ago by
Ram
43k • written 3.2 years ago by
A_heath
▴ 160
22
votes
16
replies
12k
views
6 follow
List All The Tools Or Write A Script To Validate That A Sequence Only Contains Letters From A Given Alphabet
dna
sequence
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Biostar User
★ 1.0k
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 18 days ago by
bk11
★ 2.4k • written 9 weeks ago by
Sofia
• 0
37
votes
16
replies
4.0k
views
9 follow
Forum:
Sanger sequencing is no longer the gold standard?
Sanger
NGS
updated 12 months ago by
Ram
43k • written 6.5 years ago by
lamteva.vera
▴ 220
1,000 results • Page
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Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
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Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
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pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
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dlera.lozano
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Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
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Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
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43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
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Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
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GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
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You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R
by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran
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142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
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There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file?
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wyuan37
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Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file?
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wyuan37
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Thanks! Super helpful.
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1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
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