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684 results • Page
3 of 14
Sort: replies
Rank
Views
Votes
Replies
0
votes
5
replies
707
views
vcftools --weir-fst-pop returns -nan
fst
vcftools
updated 6 days ago by
mingxi
• 0 • written 5 months ago by
elizabeth
• 0
8
votes
5
replies
352
views
I don't want to believe the Interproscan DB estimated download time.
Interproscan
4 days ago by
gh
• 0
1
vote
5
replies
1.2k
views
Forum:
PhD: Research interest or better program?
PhD
updated 4 days ago by
Ram
39k • written 4.0 years ago by
Sslero
• 0
3
votes
5
replies
2.9k
views
GISTIC 2.0 markers
segmentation
marker
cnv
gistic
updated 2 days ago by
Ram
39k • written 3.7 years ago by
enho
▴ 40
2
votes
5
replies
414
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
6 days ago by
DanielEB_fisk
• 0
3
votes
5
replies
1.7k
views
Remap GRCh38.p13 to GRCh38
haplotype
bed
genome
freeze
map
updated 3 days ago by
Jeremy Leipzig
21k • written 2.2 years ago by
schmau
▴ 10
1
vote
5
replies
2.3k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping
R
time-series
updated 5 days ago by
Ram
39k • written 5.2 years ago by
fi1d18
★ 4.2k
5
votes
5
replies
196
views
Alignment of case vs. control from different origin
Alignment
RNAseq
1 hour ago by
sativus
• 0
0
votes
5
replies
362
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 2 days ago by
Joe
21k • written 3 days ago by
gunala.nikhil
• 0
1
vote
4
replies
572
views
Expected number of haplotype IDs per path in PHG
PHG
updated 5 days ago by
Ram
39k • written 6 weeks ago by
twrl8
• 0
1
vote
4
replies
1.5k
views
Time series event recurrence comparison
recurrence
time-series
updated 5 days ago by
Ram
39k • written 6.7 years ago by
Nicolas Rosewick
10k
1
vote
4
replies
189
views
Dot Plot using KEGG
KEGG
DotPlot
GO
4 days ago by
smanzano250800
• 0
1
vote
4
replies
2.4k
views
Running SortMeRNA for bulk RNAseq data
sortmerna
RNA-Seq
updated 3 days ago by
Ram
39k • written 3.9 years ago by
Farah
▴ 80
0
votes
4
replies
789
views
Detecting Biomarkers from Time Series Gene Epression data
Time-Series
Gene-Expression
Biomarkers
updated 6 days ago by
Ram
39k • written 3.1 years ago by
donnieDarko
• 0
4
votes
4
replies
287
views
Optimum setting for local blastp for ~10K sequences
blast
blastp
hpc
41 minutes ago by
sodiumnitrate
▴ 20
3
votes
4
replies
225
views
how to use nohup with parallel
parallel
nohup
updated 6 days ago by
GenoMax
129k • written 6 days ago by
gavin
• 0
13
votes
4
replies
7.9k
views
Selection of a "suggestive" level of association in a GWAS study
association
GWAS
statistics
4 days ago by
Vincent Laufer
★ 2.9k
0
votes
4
replies
328
views
What are recommended parameters for the local protein alignment ?
protein
alignment
1 day ago by
Alexander
▴ 70
2
votes
4
replies
198
views
MACS2 peak calling
MACS2
peak-calling
updated 4 days ago by
seidel
11k • written 5 days ago by
Maurice
• 0
0
votes
4
replies
266
views
Identification of genes involved in my pathway
KEGG
keggGet
3 days ago by
smanzano250800
• 0
10
votes
4
replies
5.4k
views
Forum:
Bioinformatics: Which language should I learn
programming
updated 5 days ago by
Ram
39k • written 4.1 years ago by
MEHAR ALI RAZA
• 0
2
votes
4
replies
316
views
PacBio Pipeline and Tools for Variant Call
longread
pacbio
whatshap
pbmm2
3 days ago by
Kiran
▴ 80
0
votes
4
replies
1.7k
views
Forum:
Multiple Sequence Alignment Applications
snp
updated 3 days ago by
Ram
39k • written 3.9 years ago by
manimphil89
• 0
4
votes
4
replies
278
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 3 days ago by
ATpoint
72k • written 3 days ago by
bioinfo
▴ 80
4
votes
4
replies
359
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 6 days ago by
Joe
21k • written 10 days ago by
antoine.fauchois92
▴ 20
1
vote
4
replies
233
views
How to calculate TPM from featureCounts output
rna
featurecounts
counts
rna-seq
length
updated 1 day ago by
rpolicastro
12k • written 1 day ago by
survive
• 0
3
votes
4
replies
397
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
1 day ago by
Chris
▴ 100
0
votes
4
replies
131
views
Getting same value for start and end position, "DNA methylation"
DNAmethylation
methylkit
updated 3 hours ago by
ATpoint
72k • written 8 hours ago by
Pankaj
• 0
2
votes
4
replies
234
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 4 days ago by
Ram
39k • written 4 days ago by
miguellarrazlopezdenovales
• 0
4
votes
4
replies
1.4k
views
Forum:
When will the hg19/grch37 finally become obsolete?
Reference-Genome
updated 4 days ago by
Ram
39k • written 4.0 years ago by
gdaly9000
▴ 10
4
votes
4
replies
987
views
Forum:
What skills are required for an informatics scientist?
informatics
scientist
updated 4 days ago by
Ram
39k • written 4.0 years ago by
Shicheng Guo
★ 9.3k
1
vote
4
replies
457
views
best annotation approach for peaks
chipseeker
R
chippeakanno
updated 3 days ago by
rfran010
▴ 120 • written 21 days ago by
Chironex
▴ 40
12
votes
4
replies
1.3k
views
Forum:
Bioinformatics and biotechnology market in future.
genome
next-gen
updated 2 days ago by
Ram
39k • written 3.8 years ago by
mona11224
• 0
9
votes
4
replies
3.8k
views
Difference between Allele frequency spectrum and Joint allele frequency spectrum
allele
population structure
updated 3 days ago by
jena
▴ 260 • written 5.1 years ago by
beausoleilmo
▴ 530
0
votes
4
replies
1.3k
views
Job:
PhD position in translational clinical implementation of metagenomics
minion
bench_to_bedside
ngs
updated 3 days ago by
Ram
39k • written 3.9 years ago by
colindaven
4.8k
8
votes
4
replies
1.6k
views
News:
supporting vg users on biostars
variation-graph
genome
vg
vgteam
updated 2 days ago by
Ram
39k • written 3.7 years ago by
Erik Garrison
★ 2.4k
3
votes
4
replies
271
views
bcftools "--filter-logic" flag, what + means?
bcftools
vcf
updated 6 hours ago by
raphael.B
▴ 360 • written 3 days ago by
Eugene A
▴ 170
13
votes
4
replies
983
views
Forum:
The shortcoming of shiny app in building webserver
R
shiny
webserver
updated 2 days ago by
Ram
39k • written 3.7 years ago by
harrypotterandsbt
▴ 110
1
vote
4
replies
2.1k
views
How to extract the first and last N bases from a read in a fastq file?
fastq
updated 5 days ago by
Ram
39k • written 4.1 years ago by
lovegenetics
▴ 70
5
votes
4
replies
1.5k
views
Detection of DE genes among different tissues of an organism during time - RNA seq
detection
DE-genes
multi-treatments
time-series
updated 5 days ago by
Ram
39k • written 6.9 years ago by
statfa
▴ 720
11
votes
4
replies
333
views
how to sort a fasta file
fasta
updated 3 days ago by
Pierre Lindenbaum
154k • written 4 days ago by
Mohd
▴ 20
2
votes
3
replies
663
views
Forum:
What are the major types of choices that affect an analysis?
reproducibility
updated 5 days ago by
Ram
39k • written 4.1 years ago by
Jeremy Leipzig
21k
0
votes
3
replies
171
views
Convert Bam file to Fastq
Fastq
Bam
to
updated 11 hours ago by
GenoMax
129k • written 16 hours ago by
وفاء
• 0
0
votes
3
replies
426
views
ABySS genome assembler
ABySS
genome
k-mers
assembly
updated 6 days ago by
shelkmike
▴ 920 • written 9 days ago by
npavliukovec
• 0
0
votes
3
replies
1.1k
views
Building multiple consensus sequences from multiple fasta sequences
next-gen-sequencing
sequence
alignment
updated 3 days ago by
Ram
39k • written 3.9 years ago by
miss
• 0
13
votes
3
replies
25k
views
What is the difference between blastx and tblastn?
assembly
blast
ncbi
sequence
updated 4 days ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
1
vote
3
replies
183
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 4 days ago by
Pierre Lindenbaum
154k • written 5 days ago by
herh
• 0
1
vote
3
replies
2.3k
views
Time series microarray data
microarray
cancer
time-series
updated 5 days ago by
Ram
39k • written 6.8 years ago by
Andrea
▴ 60
1
vote
3
replies
785
views
DESEQ2 Time Course Data
DESEQ2
RNA-Seq
TIME-SERIES
updated 5 days ago by
Ram
39k • written 3.3 years ago by
tirza.doniger
▴ 10
1
vote
3
replies
331
views
Make a BedGraph file
BedGraph
RepeatMasker
BED
4 hours ago by
kirillkirilenko
▴ 10
684 results • Page
3 of 14
Recent Votes
Comment: If RNA-seq includes miRNA genes then why are there miRNA specific pipelines?
should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential expression analysis
During RNA-seq analysis a lot of pseudogenes come up as DE
Answer: How to calculate TPM from featureCounts output
A: Problem regarding Software installation.
Answer: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
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Comment: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex
by
Kermit
▴ 80
See also: https://www.biostars.org/p/9535550/#9536086
Answer: Getting species names and taxa id from assembly accession number
by
MirianT_NCBI
▴ 580
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
Answer: Installation of PPFinder
by
GenoMax
129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output
by
rpolicastro
12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl
by
ATpoint
72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin
by
sativus
• 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis
by
nux
▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
Comment: CNNScoreVariants Error
by
bestone
▴ 10
Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG
by
jrodrigu
• 0
Thank you so much. I made the suggested changes. However, I still have the same problem. Please check the new log file. https://github.c…
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation"
by
bioinfo_ga
▴ 50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output
by
bioinfo_ga
▴ 50
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
biofalconch
▴ 580
Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
biofalconch
▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
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