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546 results • Page
1 of 11
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 4 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 4 days ago by
dare_devil
★ 3.1k • written 5.3 years ago by
win
▴ 940
1
vote
4
replies
4.8k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R
heatmap
updated 14 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 18 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 4 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 14 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 17 days ago by
Ram
39k • written 5.7 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 4 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 10 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 18 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 2 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 18 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 16 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 17 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 11 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
6
votes
6
replies
2.6k
views
ChIP-Seq Intensity Analysis
R
ChIP-Seq
updated 16 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 18 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 4 days ago by
Ram
39k • written 5.8 years ago by
The
▴ 180
2
votes
8
replies
2.6k
views
How to convert a database from protein to nucleotide
blastn
unix
blastx
blast
updated 23 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 10 days ago by
Ram
39k • written 5.0 years ago by
wocana
▴ 20
1
vote
10
replies
2.5k
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 7 days ago by
Ram
39k • written 4.2 years ago by
Kumar
▴ 100
0
votes
0
replies
2.5k
views
Are secondary alignments (SAM) produced by STAR aligner linked with MAPQ score?
alignment
RNA-Seq
updated 22 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 11 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
1
vote
1
reply
2.5k
views
Hmmer Alignment input parse error
alignment
hmmer
updated 21 days ago by
Ram
39k • written 5.9 years ago by
hivemind
▴ 20
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 18 days ago by
Ram
39k • written 7.2 years ago by
rachelrodgers12
▴ 10
3
votes
4
replies
2.4k
views
Unable to install Autogrid4
autogrid
software-error
autogrid4
updated 16 days ago by
Ram
39k • written 2.2 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 21 hours 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 18 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 4 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 2 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 21 days ago by
Ram
39k • written 2.3 years ago by
thitrucminh.nguyen
• 0
0
votes
2
replies
2.2k
views
Error while running MEGAX
multiple-sequence-alignment
MEGAX
updated 18 days ago by
Ram
39k • written 5.0 years ago by
Mohak
▴ 20
0
votes
4
replies
2.1k
views
picard markduplicate output smaller file
picard
markduplicates
gatk
updated 8 days ago by
Ram
39k • written 4.4 years ago by
Peter Chung
▴ 190
3
votes
12
replies
2.1k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 1 day ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
5
replies
2.0k
views
error during installationi of KisSplice
cpp
c
RNA-Seq
kissplice
SNP
updated 12 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 12 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 21 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 24 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 16 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 1 day 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 18 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 8 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 17 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 8 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 4 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 12 days ago by
Ram
39k • written 5.3 years ago by
michael.nagle
▴ 100
1
vote
1
reply
1.6k
views
Bioinformatics tools for Plasmid detection
short-read
plasmid
updated 2 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 18 days ago by
Ram
39k • written 5.8 years ago by
Anima Mundi
★ 2.9k
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 21 days ago by
Ram
39k • written 2.2 years ago by
dlsublime
• 0
3
votes
7
replies
1.6k
views
align_and_estimate_abundance error Trinty
align_and_estimate_abundance
RNA-SEQ
RSEM
Trinity
updated 19 days ago by
Ram
39k • written 20 months ago by
Princy
▴ 60
546 results • Page
1 of 11
Recent Votes
A: Single end or paired end for variant calling
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Bioinformatics data integration
Answer: Hiplot: a simple and user-friendly visualization platform for scientific data
Multiomics data preprocessing
Comment: Low mapping percentage
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Comment: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
by
Mustafa
• 0
Thank you so much ! will try them all !
Answer: I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
by
andres.firrincieli
3.3k
If the fasta file contains the genome sequence you can use the following: 1. GToTree (see example [here][1]) 2. [GTDB-tk][2] *de novo…
Comment: Low mapping percentage
by
Sib
▴ 40
Thank you for the reply @genomax . If there is not much I can do about the contamination at this stage, what is the benefit of knowing the…
Answer: integrate single cell RNA sequencing data
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Hamid Ghaedi
2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP
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Vincent Laufer
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@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline
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Chris
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Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs
by
rycro_c
• 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage
by
Dave Carlson
★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order?
by
Pierre Lindenbaum
154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage
by
GenoMax
129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences
by
GenoMax
129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files
by
Joe
21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
GenoMax
129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order?
by
GenoMax
129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
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