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525 results • Page
4 of 11
Sort: Views
Rank
Views
Votes
Replies
0
votes
9
replies
462
views
Low number of both surviving reads after trimming
trimmomatic
trimming
21 days ago by
Jay
• 0
1
vote
5
replies
456
views
Haddock 2.4
Protein
Docking
updated 29 days ago by
dthorbur
★ 1.9k • written 4 weeks ago by
Preeti
• 0
0
votes
1
reply
447
views
principal coordinate analysis
PCoA
R
updated 16 days ago by
Ram
43k • written 10 months ago by
rene.j.erhardt
▴ 20
1
vote
1
reply
446
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 10 days ago by
chrchang523
10k • written 10 days ago by
dsbusiness135
▴ 10
0
votes
6
replies
442
views
Download Panther entry list
PANTHER
28 days ago by
Nicolas
• 0
0
votes
0
replies
440
views
Tools for identifying trans-splicing from long read data
long-read
splicing
nanopore
trans-splicing
updated 13 days ago by
Ram
43k • written 13 months ago by
dthorbur
★ 1.9k
0
votes
3
replies
438
views
How do I get the gene annotations as a text file from a genbank file?
sequence-annotation
genbank
updated 20 days ago by
Ram
43k • written 20 days ago by
eae6d2e7
• 0
0
votes
6
replies
435
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
8 days ago by
marongiu.luigi
▴ 710
0
votes
0
replies
408
views
Pairwise alignment of two long chromosomes (~100Mbp) with lastz
lastz
alignment
updated 13 days ago by
Ram
43k • written 20 months ago by
vahe.galstyan
• 0
1
vote
1
reply
407
views
Long reads Annotation
long-reads
pacbio
updated 13 days ago by
Ram
43k • written 2.1 years ago by
Gerardo
• 0
0
votes
4
replies
405
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
19 hours ago by
feather-W
• 0
0
votes
5
replies
402
views
Error running local blastn in R using system2
blastn
NCBI
R
20 days ago by
Harrison
• 0
3
votes
5
replies
391
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
updated 15 days ago by
GenoMax
141k • written 16 days ago by
e.r.zakiev
▴ 190
0
votes
7
replies
389
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 22 days ago by
GenoMax
141k • written 22 days ago by
Patadu94
• 0
0
votes
4
replies
388
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
21 days ago by
BRENO
• 0
0
votes
0
replies
388
views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately…
normal
inverse
transformation
7 days ago by
Isaac
• 0
5
votes
6
replies
382
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 16 days ago by
Istvan Albert
100k • written 17 days ago by
Pumla
• 0
0
votes
7
replies
382
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 13 days ago by
Papyrus
★ 2.9k • written 14 days ago by
doramora
▴ 10
2
votes
6
replies
376
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
10 days ago by
jkim
▴ 170
0
votes
0
replies
374
views
Realistic RNA-seq using Polyester + Differences between Hexamer bias and positional bias?
polyester
short-read
bias
updated 16 days ago by
Ram
43k • written 17 months ago by
shinyjj
▴ 50
1
vote
4
replies
373
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 5 days ago by
BioinfGuru
★ 1.7k • written 6 days ago by
Morteza
• 0
1
vote
3
replies
373
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 10 days ago by
Ram
43k • written 13 days ago by
catherinemaria2728
• 0
0
votes
0
replies
372
views
SNV occuring 2 fold more in forward than in reverse reads should be filtered?
Variant-Calling
updated 23 days ago by
Ram
43k • written 2.3 years ago by
jeni
▴ 90
0
votes
5
replies
372
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 8 days ago by
GenoMax
141k • written 9 days ago by
Shay
• 0
2
votes
4
replies
370
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 8 days ago by
GenoMax
141k • written 9 days ago by
pl.terzian
• 0
0
votes
0
replies
367
views
The chromatin accessibility in regulatory regions of the rhodopsin gene RHO.
ATAC-Seq
updated 16 days ago by
Ram
43k • written 2.6 years ago by
madhubioinform
• 0
2
votes
2
replies
367
views
Would you recommend me any tool to assign protein family membership to an aminoacidic fasta file?
protein-annotation
fasta
updated 29 days ago by
Dunois
★ 2.5k • written 10 weeks ago by
v.berriosfarias
▴ 140
0
votes
1
reply
365
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 11 hours ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
1
vote
0
replies
364
views
Differential expression analysis on multiple integrated datasets
microarray
Z-score
limma
differential-gene-expression
meta-analysis
updated 9 days ago by
Ram
43k • written 2.3 years ago by
michael.s
▴ 10
0
votes
2
replies
363
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
18 days ago by
Samuel
▴ 20
0
votes
5
replies
360
views
Parsing fasta file by coordinates
linux
fasta
updated 21 days ago by
GenoMax
141k • written 24 days ago by
sorrymouse
▴ 120
0
votes
5
replies
360
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
14 days ago by
Srinka
▴ 20
0
votes
3
replies
351
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 8 hours ago by
GenoMax
141k • written 1 day ago by
Kai Xin
• 0
0
votes
0
replies
348
views
Benchmarking pipeline for Variant identification using RNA-seq data
RNA-seq
somatic
Variant-calling
germline
updated 23 days ago by
Ram
43k • written 18 months ago by
ahkam.s
• 0
4
votes
4
replies
348
views
Average expression of a sample in single-cell data
single-cell
rna-seq
16 days ago by
newuser2024
• 0
1
vote
4
replies
343
views
Molecular docking with Autodock
Docking
proteomics
updated 13 days ago by
Ram
43k • written 11 weeks ago by
shwetamgr1
▴ 10
1
vote
3
replies
341
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 17 days ago by
Pierre Lindenbaum
161k • written 18 days ago by
Max
• 0
2
votes
5
replies
335
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
1 day ago by
Bikram Kumar
• 0
1
vote
4
replies
335
views
How to get human-mouse conservation score from UCSC
conservation
mouse
IGV
human
score
13 days ago by
diqixiaoyaoer
▴ 10
3
votes
4
replies
334
views
Single cell analysis with "meta".tsv.gz file
Single-cell
16 days ago by
Estevão
• 0
0
votes
3
replies
329
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
27 days ago by
kabir.deb
▴ 80
0
votes
0
replies
329
views
Looking to improve my understanding of Homer's mergePeaks function: unclear of how the merged file is created?
Homer
ATACseq
14 days ago by
Ronin
• 0
0
votes
2
replies
328
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 23 days ago by
Ram
43k • written 8 weeks ago by
maplewj
▴ 10
0
votes
3
replies
326
views
Resources regarding Proteomics (In-Silico)
molecular-simulation
docking
protein
proteomics
updated 16 days ago by
Ram
43k • written 4 weeks ago by
Saurabh
• 0
2
votes
2
replies
326
views
Seeking help with Tcga Target Gtex Expected Count Data
R
TCGA
gTEX
26 days ago by
bioinfo_enthusiast
• 0
0
votes
2
replies
322
views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation
models
gif
gene
cgi
17 days ago by
O.rka
▴ 710
1
vote
5
replies
322
views
samtools filtering
samtools
updated 7 days ago by
jkbonfield
★ 1.2k • written 15 days ago by
sansan_96
▴ 80
0
votes
0
replies
321
views
GTEx long read data
short-read
long-read
gtex
updated 13 days ago by
Ram
43k • written 18 months ago by
shinyjj
▴ 50
1
vote
2
replies
318
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 15 days ago by
jkbonfield
★ 1.2k • written 4 weeks ago by
geocarvalho
▴ 360
0
votes
4
replies
318
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 7 days ago by
GenoMax
141k • written 9 days ago by
Soohyun
• 0
525 results • Page
4 of 11
Recent Votes
Answer: Korean reference file
Comment: Korean human genome reference file
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
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Recent Replies
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
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