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110,336 results • Page
1 of 2207
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Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
1 minute ago by
saladi1
▴ 30
2
votes
4
replies
177
views
I don't want to believe the Interproscan DB estimated download time.
Interproscan
updated 1 hour ago by
Mensur Dlakic
★ 23k • written 20 hours ago by
gh
• 0
1
vote
2
replies
183
views
What is the best way to clean bulk RNA-seq data?
normalization
TPM
r
updated 4 hours ago by
swbarnes2
13k • written 1 day ago by
JACKY
▴ 80
0
votes
1
reply
101
views
Make a BedGraph file
BedGraph
RepeatMasker
BED
updated 4 hours ago by
bhumm
▴ 40 • written 17 hours ago by
kirillkirilenko
▴ 10
1
vote
7
replies
138
views
RNAseq Data and Pipeline
RNA-Seq
DESeq2
Differential-Gene-Expression
updated 5 hours ago by
Ram
39k • written 5 hours ago by
turcoa1
• 0
0
votes
2
replies
550
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 6 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
394
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 7 hours ago by
Zhenyu Zhang
▴ 800 • written 3 days ago by
Camilo Andres
▴ 30
0
votes
2
replies
76
views
gatk Hardfilter Error
hardfilter
updated 7 hours ago by
Pierre Lindenbaum
154k • written 7 hours ago by
bestone
▴ 10
0
votes
3
replies
104
views
How to make a dotplot for bulk RNA average expression ?
Dotplot
RNA-seq
updated 40 minutes ago by
bhumm
▴ 40 • written 8 hours ago by
LionisOne
• 0
0
votes
1
reply
66
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 8 hours ago by
andres.firrincieli
3.3k • written 8 hours ago by
kamanovae
▴ 80
0
votes
1
reply
79
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 5 hours ago by
GenoMax
129k • written 8 hours ago by
fafad046
• 0
3
votes
6
replies
165
views
Salmon Index
transcriptomics
Bulk
RNA-sequencing
updated 5 hours ago by
GenoMax
129k • written 8 hours ago by
ashleymb1116
• 0
1
vote
4
replies
515
views
Expected number of haplotype IDs per path in PHG
PHG
updated 9 hours ago by
Ram
39k • written 5 weeks ago by
twrl8
• 0
0
votes
6
replies
225
views
how to create correlation matrix R
pearson-correlation
R
updated 10 hours ago by
GenoMax
129k • written 16 hours ago by
satva72
• 0
0
votes
1
reply
74
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
updated 10 hours ago by
GenoMax
129k • written 10 hours ago by
Mohd
• 0
0
votes
1
reply
71
views
sorting BAM file
BAM
updated 9 hours ago by
Ram
39k • written 10 hours ago by
Mohammad Amin
• 0
0
votes
1
reply
63
views
Search SRA metadata for Histological_Type and Body_Site
sra
updated 10 hours ago by
GenoMax
129k • written 11 hours ago by
oakhamwolf
▴ 20
2
votes
3
replies
161
views
NCBI refseq ids to uniprot ids
refseq
Uniprot
updated 3 hours ago by
Ram
39k • written 15 hours ago by
t.ali
• 0
1
vote
3
replies
111
views
Covert multiple short sequence into list of IUPAC motif
sequence
updated 10 hours ago by
GenoMax
129k • written 12 hours ago by
praasu
▴ 40
1
vote
0
replies
53
views
Resequencing data of pangenome
NGS
PanGenome
Resequence
updated 5 hours ago by
Ram
39k • written 13 hours ago by
bioinfo223
▴ 10
3
votes
2
replies
138
views
Graphing Average Expression of Group of Genes
Boxplot
R
updated 8 hours ago by
Shred
★ 1.2k • written 18 hours ago by
cthangav
▴ 40
0
votes
0
replies
50
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 13 hours ago by
zx8754
11k • written 13 hours ago by
sidrah.maryam
▴ 50
0
votes
1
reply
69
views
Seurat: How to get all genes name of a cell ?
seurat
updated 2 hours ago by
jv
★ 1.2k • written 13 hours ago by
Picasa
▴ 640
1
vote
0
replies
108
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 3 hours ago by
Ram
39k • written 15 hours ago by
Supernova
• 0
0
votes
0
replies
72
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 10 hours ago by
Ram
39k • written 15 hours ago by
Fred
• 0
0
votes
1
reply
238
views
CORUM server not working?
corum
protein
complexes
database
updated 16 hours ago by
Elisabeth Gasteiger
★ 2.2k • written 11 days ago by
marta
• 0
0
votes
0
replies
79
views
Job:
PhD students in Data Science - DTU Biosustain
PhD
Biology
Data-Science
updated 5 hours ago by
Ram
39k • written 17 hours ago by
info
▴ 70
0
votes
3
replies
211
views
1000G reference panel for LD
plink
gwas
LD
19 hours ago by
en_keser
• 0
0
votes
1
reply
115
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 10 hours ago by
Ram
39k • written 19 hours ago by
chengc2016zzu
• 0
3
votes
4
replies
170
views
how to use nohup with parallel
parallel
nohup
updated 13 hours ago by
GenoMax
129k • written 21 hours ago by
gavin
• 0
0
votes
0
replies
66
views
Michigan Imputation Server - Local docker image
genotype
WGS
imputation
19 hours ago by
batch_effect
• 0
1
vote
1
reply
109
views
How do I restrict to only hm3 SNPs for plink analyses?
plink
hm3
updated 21 hours ago by
chrchang523
10k • written 1 day ago by
garrett.ennis
• 0
0
votes
0
replies
63
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
21 hours ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
151
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
8 hours ago by
Pegasus
▴ 90
0
votes
0
replies
93
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
234
views
how to intersect multiple bed files and get results in uncollapsed genomic intervals
bedtools
bedops
intervals
genomic
intersect
9 hours ago by
Alewa
▴ 110
0
votes
0
replies
97
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
386
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
150
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
138
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
updated 6 hours ago by
Jesse
▴ 540 • written 1 day ago by
J.F.Jiang
▴ 900
0
votes
2
replies
172
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
676
views
Regular Expression for conversion
Linux
grep
updated 9 hours ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
1
reply
141
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 3 hours ago by
Ram
39k • written 1 day ago by
barrypraveen
▴ 110
1
vote
2
replies
246
views
Retrieving allele-specific information for a variant using VEP annotation
variant-calling
VEP
COSMIC
updated 1 day ago by
Ram
39k • written 2 days ago by
bt_cepo
▴ 20
0
votes
1
reply
302
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
189
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
167
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
7
votes
5
replies
366
views
6 follow
Unusual FASTQ file
fastqc
fastq
RNAseq
updated 3 hours ago by
Ram
39k • written 2 days ago by
Nada
• 0
110,336 results • Page
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Recent Votes
Answer: NCBI refseq ids to uniprot ids
Answer: NCBI refseq ids to uniprot ids
Comment: Unusual FASTQ file
Answer: Graphing Average Expression of Group of Genes
Comment: Graphing Average Expression of Group of Genes
How to create specific .bed files for a panel of genes
Answer: How do you add an ORF that overlaps the two regions where a circular genome is c
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Answer: I don't want to believe the Interproscan DB estimated download time.
by
Mensur Dlakic
★ 23k
With [**aria2**][1] and multiple connections, I download at ~2.2MiB. The estimate is still ~190 hours. aria2c --continue=true --max-…
Comment: Seurat: How to get all genes name of a cell ?
by
jv
★ 1.2k
if you want the genes in your count matrix use `rownames(obj)`. Or are you looking to get all genes with count > 0 for a particular cell? P…
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?
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