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565 results • Page
1 of 12
Sort: Views
Rank
Views
Votes
Replies
3
votes
16
replies
9.9k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 7 days ago by
Ram
39k • written 4.2 years ago by
Star
▴ 60
1
vote
7
replies
5.6k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 8 days ago by
dare_devil
★ 3.1k • written 5.4 years ago by
win
▴ 940
0
votes
4
replies
5.0k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 1 day ago by
Franco
• 0 • written 5.6 years ago by
ac.research
▴ 30
1
vote
4
replies
4.9k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R
heatmap
updated 18 days ago by
Ram
39k • written 5.3 years ago by
chetana
▴ 60
0
votes
4
replies
4.8k
views
Sequence alignment length
multiple-sequence-alignment
updated 21 days ago by
Ram
39k • written 6.3 years ago by
biobudhan
▴ 20
7
votes
7
replies
4.4k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 7 days ago by
Ram
39k • written 4.4 years ago by
stu111538
▴ 80
3
votes
4
replies
3.8k
views
What are the Pros and Cons of working in Bioinformatics???
career
bio
updated 18 days ago by
Ram
39k • written 5.3 years ago by
scottschu97
▴ 20
0
votes
4
replies
3.7k
views
What is Dunn's multiple comparison test?
statistics
updated 21 days ago by
Ram
39k • written 5.8 years ago by
Koreanraichu
• 0
1
vote
5
replies
3.6k
views
Time-series or pairwise comparison EdgeR - what's more suited?
DGE-analysis
Time-series
pairwise
updated 7 days ago by
Ram
39k • written 6.8 years ago by
Biogeek
▴ 470
0
votes
16
replies
3.2k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 14 days ago by
Ram
39k • written 5.0 years ago by
rororo
• 0
0
votes
0
replies
3.1k
views
Find conserved blocks and extract subalignment with Python
multiple-sequence-alignment
python
updated 21 days ago by
Ram
39k • written 6.1 years ago by
Kevin D
▴ 30
1
vote
1
reply
3.1k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 6 days ago by
sackettl
▴ 20 • written 7.0 years ago by
maria.segovia.ramirez
▴ 10
0
votes
5
replies
3.1k
views
Phylogeny Heatmap with Python
multiple-sequence-alignment
updated 21 days ago by
Ram
39k • written 4.2 years ago by
marina.gerges
• 0
0
votes
12
replies
2.9k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 20 days ago by
Ram
39k • written 5.6 years ago by
fonteneaudam
▴ 20
0
votes
3
replies
2.9k
views
From FASTQ to clean BAM using GATK tutorial #6484
gatk
MergeBamAlignment
uBAM
bamclipper
updated 20 days ago by
Ram
39k • written 5.6 years ago by
lamteva.vera
▴ 220
1
vote
14
replies
2.8k
views
How to convert Haplotypes file to PLINK format data
R
plink
updated 14 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
6
votes
6
replies
2.7k
views
ChIP-Seq Intensity Analysis
R
ChIP-Seq
updated 20 days ago by
Ram
39k • written 5.5 years ago by
solveforj
▴ 20
1
vote
3
replies
2.6k
views
Multiple Sequence Alignment Python
multiple-sequence-alignment
ClustalW
Biopython
updated 21 days ago by
Ram
39k • written 5.1 years ago by
Manu Madhavan
▴ 20
1
vote
1
reply
2.6k
views
Comparing time series expression data
time-series
gene-expression
updated 7 days ago by
Ram
39k • written 5.8 years ago by
The
▴ 180
1
vote
10
replies
2.6k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 11 days ago by
Ram
39k • written 4.2 years ago by
Kumar
▴ 100
2
votes
8
replies
2.6k
views
How to convert a database from protein to nucleotide
blastn
unix
blastx
blast
updated 26 days ago by
Ram
39k • written 6.2 years ago by
AJTrunkskun94
• 0
1
vote
4
replies
2.5k
views
DBD::mysql::st execute failed: The table 'InplgOrthoInplg
orthomcl
ortho
ubuntu
mysql
updated 13 days ago by
Ram
39k • written 5.0 years ago by
wocana
▴ 20
0
votes
0
replies
2.5k
views
Are secondary alignments (SAM) produced by STAR aligner linked with MAPQ score?
alignment
RNA-Seq
updated 26 days ago by
Ram
39k • written 6.2 years ago by
Claudio
• 0
0
votes
2
replies
2.5k
views
How to get Haplotype file from PLINK format data
SNP
PLINK
updated 15 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
1
vote
0
replies
2.5k
views
Running Multiple Alignments in MEGA with a script produces errors.
next-gen
RNA-Seq
MEGA
multiple-alignment
updated 21 days ago by
Ram
39k • written 7.3 years ago by
rachelrodgers12
▴ 10
1
vote
1
reply
2.5k
views
Hmmer Alignment input parse error
alignment
hmmer
updated 25 days ago by
Ram
39k • written 6.0 years ago by
hivemind
▴ 20
3
votes
4
replies
2.4k
views
Unable to install Autogrid4
autogrid
software-error
autogrid4
updated 20 days ago by
Ram
39k • written 2.3 years ago by
roybatty269
• 0
0
votes
3
replies
2.4k
views
Generate GTF/GFF file (coordinates) from a FASTA annotated file.
Assembly
genome
updated 4 days ago by
Ram
39k • written 3.7 years ago by
marquezg48
• 0
1
vote
4
replies
2.3k
views
Using a Multiple Seq Alignment tool for pairwise alignments possible?
multiple-sequence-alignment
msa
alignment
updated 21 days ago by
Ram
39k • written 7.1 years ago by
nchuang
▴ 260
1
vote
5
replies
2.3k
views
Calculating distance matrix of RNA-seq data
Dynamic-Time-Warping
R
time-series
updated 7 days ago by
Ram
39k • written 5.2 years ago by
fi1d18
★ 4.2k
4
votes
7
replies
2.2k
views
low bootstrap value?
phylogeny
genome
alignment
updated 6 days ago by
Ram
39k • written 4.0 years ago by
Kumar
▴ 100
0
votes
7
replies
2.2k
views
How much time should be expected for building a database by kraken2-build?
kraken2
updated 25 days ago by
Ram
39k • written 2.4 years ago by
thitrucminh.nguyen
• 0
0
votes
2
replies
2.2k
views
Error while running MEGAX
multiple-sequence-alignment
MEGAX
updated 21 days ago by
Ram
39k • written 5.0 years ago by
Mohak
▴ 20
3
votes
12
replies
2.2k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 5 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
4
replies
2.1k
views
picard markduplicate output smaller file
picard
markduplicates
gatk
updated 11 days ago by
Ram
39k • written 4.4 years ago by
Peter Chung
▴ 190
0
votes
5
replies
2.0k
views
error during installationi of KisSplice
cpp
c
RNA-Seq
kissplice
SNP
updated 15 days ago by
Ram
39k • written 6.8 years ago by
yoyofangliu
• 0
1
vote
2
replies
2.0k
views
Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
vcftools
samtools
faidx
tabix
1000Genomes
updated 15 days ago by
barslmn
★ 1.6k • written 5.6 years ago by
shrutishreyajha
▴ 10
1
vote
3
replies
1.8k
views
Translate from hsa-let- to MIMAT type
conversion
updated 25 days ago by
Ram
39k • written 6.0 years ago by
landscape95
▴ 190
0
votes
0
replies
1.8k
views
IDBA-UD Parameters for Bio Linux?
Linux
Bio
parameters
IDBA-UD
updated 27 days ago by
Ram
39k • written 6.2 years ago by
Seot
• 0
3
votes
6
replies
1.8k
views
Biopython TimeExceptionError how to handle?
biopython
entrez
updated 20 days ago by
Ram
39k • written 5.6 years ago by
Xylanaser
▴ 80
2
votes
1
reply
1.8k
views
How do I apply a patch to hg38?
reference
human
freeze
hg38
patch
updated 5 days ago by
Jeremy Leipzig
21k • written 5.6 years ago by
imperialcommando117
• 0
0
votes
1
reply
1.8k
views
Get pairwise scores from alignment without re-aligning?
multiple-sequence-alignment
bit-score
alignment
updated 21 days ago by
Ram
39k • written 6.5 years ago by
mpd
• 0
3
votes
8
replies
1.7k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 12 days ago by
Ram
39k • written 4.6 years ago by
nagendranp1991
• 0
0
votes
2
replies
1.7k
views
How to process degenerate base region (DBRs) in a ddRAD sequencing protocol (remove PCR duplicates)?
ddRAD
next-gen
Stacks
DBR
updated 21 days ago by
Ram
39k • written 5.7 years ago by
beausoleilmo
▴ 530
0
votes
2
replies
1.7k
views
Fourfold degenerate codons in VCF File
vcf
genome
updated 11 days ago by
Ram
39k • written 4.4 years ago by
crippa.to
• 0
0
votes
0
replies
1.7k
views
Artificial Neural Networks applied to environmental data
artificial-neural-networks
time-series
ANN
updated 7 days ago by
Ram
39k • written 8.6 years ago by
felipehcoutinho
▴ 10
0
votes
4
replies
1.6k
views
Extra header column stopping EMMAX (C), but not seen in input files
emmax
genomics
Cpp
plink
GWAS
updated 15 days ago by
Ram
39k • written 5.3 years ago by
michael.nagle
▴ 100
0
votes
2
replies
1.6k
views
Need help with error fromTOMplot network heatmap: "Error in x[, iy] : subscript out of bounds"
WGCNA
TOMplot
updated 25 days ago by
Ram
39k • written 2.2 years ago by
dlsublime
• 0
1
vote
1
reply
1.6k
views
Bioinformatics tools for Plasmid detection
short-read
plasmid
updated 5 days ago by
Ram
39k • written 3.9 years ago by
El Niño
▴ 10
1
vote
2
replies
1.6k
views
Learning some Drop-Seq as a first approach to RNA-Seq while on vacation
hardware
RNA-Seq
drop-seq
updated 22 days ago by
Ram
39k • written 5.8 years ago by
Anima Mundi
★ 2.9k
565 results • Page
1 of 12
Recent Votes
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
Answer: Alignment of case vs. control from different origin
Comment: Alignment of case vs. control from different origin
Comment: Gene prediction software
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Recent Replies
Comment: Differential protein expression analysis
by
Ribo
▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, your code isn't correct. You are testing an intercept equal to zero instead of testing for a logFC. I wonder what comparison you were t…
Answer: Extract sequences from a fastq file by a list of IDs
by
GenoMax
129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Yeah, I added the design matrix. `design <- model.matrix(~0+group)`. These are raw counts.
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Ayish
• 0
Thank you for reply. I have Illumina paired-end reads. Would it be fine if I use hard-masking for STAR and soft-masked genome for BRAKER2? …
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
Soft masking the genome (unless something changed) not make any difference for STAR. Depending on how your RNA-Seq is done (Illumina? paire…
Answer: How to handle NaN in emmax Kinship matrix?
by
Thu
• 0
Hi! Thanks for sharing your solution! It works! :)
Comment: Gene prediction software
by
Darked89
4.4k
Looks like there are five Clarias genomes: * https://www.ncbi.nlm.nih.gov/genome/?term=txid13012[Organism:exp] The most complete seems t…
Comment: Alignment of case vs. control from different origin
by
sativus
▴ 10
Again, thank you so much for these very clearly explained summaries. After reading some articles on the matter, i feel i have a much better…
Answer: Extract sequences from a fastq file by a list of IDs
by
colindaven
4.9k
Some people I know have used filter-fastq successfully: https://github.com/Floor-Lab/filter-fastq
Comment: Extract sequences from a fastq file by a list of IDs
by
Pierre Lindenbaum
154k
> but none of them work for me https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs
by
Pierre Lindenbaum
154k
https://meta.stackexchange.com/questions/147616/
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
I have tried this one before but the output file is empty
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
I have tried all of them but none of them work for me
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