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110,335 results • Page
1 of 2207
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1
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157
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What is the best way to clean bulk RNA-seq data?
normalization
TPM
r
updated 1 hour ago by
swbarnes2
13k • written 1 day ago by
JACKY
▴ 80
0
votes
1
reply
81
views
Make a BedGraph file
BedGraph
RepeatMasker
BED
updated 1 hour ago by
bhumm
▴ 40 • written 14 hours ago by
kirillkirilenko
▴ 10
1
vote
7
replies
83
views
RNAseq Data and Pipeline
RNA-Seq
DESeq2
Differential-Gene-Expression
updated 2 hours ago by
Ram
39k • written 2 hours ago by
turcoa1
• 0
0
votes
2
replies
530
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 3 hours ago by
Ram
39k • written 12 months ago by
Meeran
• 0
743
votes
162
replies
113k
views
101 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 weeks ago by
Biostar
1.8k • written 6.5 years ago by
Istvan Albert
98k
0
votes
5
replies
366
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 4 hours ago by
Zhenyu Zhang
▴ 800 • written 3 days ago by
Camilo Andres
▴ 30
0
votes
2
replies
63
views
gatk Hardfilter Error
hardfilter
updated 4 hours ago by
Pierre Lindenbaum
154k • written 4 hours ago by
bestone
▴ 10
0
votes
3
replies
87
views
How to make a dotplot for bulk RNA average expression ?
Dotplot
RNA-seq
updated 45 minutes ago by
bhumm
▴ 40 • written 5 hours ago by
LionisOne
• 0
0
votes
1
reply
58
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 5 hours ago by
andres.firrincieli
3.3k • written 5 hours ago by
kamanovae
▴ 80
0
votes
1
reply
61
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 2 hours ago by
GenoMax
129k • written 5 hours ago by
fafad046
• 0
3
votes
6
replies
140
views
Salmon Index
transcriptomics
Bulk
RNA-sequencing
updated 2 hours ago by
GenoMax
129k • written 5 hours ago by
ashleymb1116
• 0
1
vote
4
replies
509
views
Expected number of haplotype IDs per path in PHG
PHG
updated 6 hours ago by
Ram
39k • written 5 weeks ago by
twrl8
• 0
0
votes
6
replies
215
views
how to create correlation matrix R
pearson-correlation
R
updated 7 hours ago by
GenoMax
129k • written 13 hours ago by
satva72
• 0
0
votes
1
reply
64
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
updated 7 hours ago by
GenoMax
129k • written 7 hours ago by
Mohd
• 0
0
votes
1
reply
66
views
sorting BAM file
BAM
updated 6 hours ago by
Ram
39k • written 7 hours ago by
Mohammad Amin
• 0
0
votes
1
reply
60
views
Search SRA metadata for Histological_Type and Body_Site
sra
updated 7 hours ago by
GenoMax
129k • written 8 hours ago by
oakhamwolf
▴ 20
0
votes
3
replies
145
views
NCBI refseq ids to uniprot ids
refseq
Uniprot
updated 53 minutes ago by
Ram
39k • written 11 hours ago by
t.ali
• 0
1
vote
3
replies
105
views
Covert multiple short sequence into list of IUPAC motif
sequence
updated 7 hours ago by
GenoMax
129k • written 9 hours ago by
praasu
▴ 40
1
vote
0
replies
47
views
Resequencing data of pangenome
NGS
PanGenome
Resequence
updated 2 hours ago by
Ram
39k • written 10 hours ago by
bioinfo223
▴ 10
1
vote
2
replies
128
views
Graphing Average Expression of Group of Genes
Boxplot
R
updated 6 hours ago by
Shred
★ 1.2k • written 15 hours ago by
cthangav
▴ 40
0
votes
0
replies
44
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 10 hours ago by
zx8754
11k • written 10 hours ago by
sidrah.maryam
▴ 50
0
votes
0
replies
54
views
Seurat: How to get all genes name of a cell ?
seurat
updated 6 hours ago by
Ram
39k • written 11 hours ago by
Picasa
▴ 640
1
vote
0
replies
89
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 40 minutes ago by
Ram
39k • written 12 hours ago by
Supernova
• 0
0
votes
0
replies
68
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 7 hours ago by
Ram
39k • written 12 hours ago by
Fred
• 0
2
votes
3
replies
158
views
I don't want to believe the Interproscan DB estimated download time.
Interproscan
updated 42 minutes ago by
Ram
39k • written 17 hours ago by
gh
• 0
0
votes
1
reply
235
views
CORUM server not working?
corum
protein
complexes
database
updated 13 hours ago by
Elisabeth Gasteiger
★ 2.2k • written 11 days ago by
marta
• 0
0
votes
0
replies
74
views
Job:
PhD students in Data Science - DTU Biosustain
PhD
Biology
Data-Science
updated 2 hours ago by
Ram
39k • written 14 hours ago by
info
▴ 70
0
votes
3
replies
207
views
1000G reference panel for LD
plink
gwas
LD
16 hours ago by
en_keser
• 0
0
votes
1
reply
108
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 7 hours ago by
Ram
39k • written 16 hours ago by
chengc2016zzu
• 0
3
votes
4
replies
162
views
how to use nohup with parallel
parallel
nohup
updated 10 hours ago by
GenoMax
129k • written 18 hours ago by
gavin
• 0
0
votes
0
replies
63
views
Michigan Imputation Server - Local docker image
genotype
WGS
imputation
16 hours ago by
batch_effect
• 0
1
vote
1
reply
105
views
How do I restrict to only hm3 SNPs for plink analyses?
plink
hm3
updated 18 hours ago by
chrchang523
10k • written 22 hours ago by
garrett.ennis
• 0
0
votes
0
replies
59
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
18 hours ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
146
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
5 hours ago by
Pegasus
▴ 90
0
votes
0
replies
90
views
Merging multiple PLINK files
plink
merging
1 day ago by
Nejla
• 0
0
votes
6
replies
1.7k
views
Using entrez-direct inside a for loop in bash
NCBI
bash
updated 1 day ago by
GenoMax
129k • written 4.2 years ago by
Lille My
▴ 30
1
vote
2
replies
228
views
how to intersect multiple bed files and get results in uncollapsed genomic intervals
bedtools
bedops
intervals
genomic
intersect
6 hours ago by
Alewa
▴ 110
0
votes
0
replies
94
views
References selected by ExomeDepth CNV
CNV
ExomeDepth
updated 1 day ago by
GenoMax
129k • written 1 day ago by
keiko.asakura
• 0
0
votes
3
replies
381
views
ABySS genome assembler
ABySS
genome
k-mers
assembly
updated 1 day ago by
shelkmike
▴ 920 • written 3 days ago by
npavliukovec
• 0
0
votes
1
reply
146
views
Perl. How to extract CDS and gene sequence in a specified interval from GenBank files?
fasta
sequence
perl
GenBank
1 day ago by
Fungi-Beware!
• 0
0
votes
1
reply
124
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
updated 3 hours ago by
Jesse
▴ 540 • written 1 day ago by
J.F.Jiang
▴ 900
0
votes
2
replies
169
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 1 day ago by
Ram
39k • written 1 day ago by
Joel Wallenius
▴ 120
1
vote
3
replies
670
views
Regular Expression for conversion
Linux
grep
updated 6 hours ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
1
reply
138
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 41 minutes ago by
Ram
39k • written 1 day ago by
barrypraveen
▴ 110
1
vote
2
replies
243
views
Retrieving allele-specific information for a variant using VEP annotation
variant-calling
VEP
COSMIC
updated 1 day ago by
Ram
39k • written 1 day ago by
bt_cepo
▴ 20
0
votes
1
reply
299
views
[Metagenome assembly] Reassembling bacterial genome using Nanopore contig/reads
illumina
nanopore
assembly
metagenome
updated 1 day ago by
Ekaterina
• 0 • written 4 weeks ago by
adhamzul
▴ 20
0
votes
2
replies
186
views
IGV grey vs white lines
minimap
nanopore
IGV
updated 1 day ago by
GenoMax
129k • written 1 day ago by
Mohd
• 0
2
votes
2
replies
163
views
featureCounts: ERROR: failed to find the gene identifier attribute
gtf
featureCounts
subread
updated 1 day ago by
GenoMax
129k • written 1 day ago by
v.berriosfarias
▴ 90
6
votes
5
replies
340
views
6 follow
Unusual FASTQ file
fastqc
fastq
RNAseq
updated 31 minutes ago by
Ram
39k • written 2 days ago by
Nada
• 0
0
votes
2
replies
150
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
1 day ago by
pg45863
• 0
110,335 results • Page
1 of 2207
Recent Votes
C: PLINK logistic regression analysis and covariates
Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
A: PolyPhen Humdiv vs HumVar discrepancies
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Comment: Unusual FASTQ file
by
Ram
39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ?
by
bhumm
▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data?
by
swbarnes2
13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Vincent Laufer
★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file
by
bhumm
▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline
by
ATpoint
72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline
by
swbarnes2
13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline
by
Ram
39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline
by
Ram
39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline
by
turcoa1
• 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree
by
GenoMax
129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline
by
Ram
39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index
by
ashleymb1116
• 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index
by
GenoMax
129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
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