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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
546
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 5 hours ago by
Ram
39k • written 12 months ago by
Meeran
• 0
0
votes
5
replies
390
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
74
views
gatk Hardfilter Error
hardfilter
updated 7 hours ago by
Pierre Lindenbaum
154k • written 7 hours ago by
bestone
▴ 10
0
votes
1
reply
63
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 7 hours ago by
andres.firrincieli
3.3k • written 8 hours ago by
kamanovae
▴ 80
0
votes
1
reply
75
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 5 hours ago by
GenoMax
129k • written 8 hours ago by
fafad046
• 0
0
votes
6
replies
224
views
how to create correlation matrix R
pearson-correlation
R
updated 9 hours ago by
GenoMax
129k • written 15 hours ago by
satva72
• 0
0
votes
1
reply
73
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
70
views
sorting BAM file
BAM
updated 8 hours ago by
Ram
39k • written 10 hours ago by
Mohammad Amin
• 0
1
vote
0
replies
52
views
Resequencing data of pangenome
NGS
PanGenome
Resequence
updated 5 hours ago by
Ram
39k • written 13 hours ago by
bioinfo223
▴ 10
0
votes
0
replies
49
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
65
views
Seurat: How to get all genes name of a cell ?
seurat
updated 1 hour ago by
jv
★ 1.2k • written 13 hours ago by
Picasa
▴ 640
1
vote
0
replies
103
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 3 hours ago by
Ram
39k • written 14 hours ago by
Supernova
• 0
0
votes
0
replies
71
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
114
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 9 hours ago by
Ram
39k • written 19 hours ago by
chengc2016zzu
• 0
0
votes
0
replies
65
views
Michigan Imputation Server - Local docker image
genotype
WGS
imputation
19 hours ago by
batch_effect
• 0
0
votes
0
replies
61
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
150
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
8 hours ago by
Pegasus
▴ 90
0
votes
0
replies
92
views
Merging multiple PLINK files
plink
merging
1 day ago by
Nejla
• 0
0
votes
0
replies
96
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
1
reply
137
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
updated 5 hours ago by
Jesse
▴ 540 • written 1 day ago by
J.F.Jiang
▴ 900
0
votes
2
replies
171
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
675
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
140
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 3 hours ago by
Ram
39k • written 1 day ago by
barrypraveen
▴ 110
0
votes
2
replies
153
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
1 day ago by
pg45863
• 0
0
votes
1
reply
131
views
ABySS Process Killed
ABySS
genome
assembly
updated 1 day ago by
GenoMax
129k • written 1 day ago by
asarcillo
• 0
0
votes
0
replies
92
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
1 day ago by
narges.bioinf
• 0
0
votes
3
replies
187
views
Query qbout single cell sequencing
fastq
ScRNA
updated 5 hours ago by
Ram
39k • written 1 day ago by
abbas.waseem.gcu
• 0
0
votes
1
reply
162
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 15 hours ago by
fracarb8
▴ 950 • written 1 day ago by
Sun
• 0
0
votes
1
reply
164
views
Why coordinate sort is required in sambamba depths?
sorting
coordinate
sambamba
linux
samtools
updated 2 days ago by
Pierre Lindenbaum
154k • written 2 days ago by
MobiusT
▴ 10
0
votes
4
replies
259
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
2 days ago by
Ahmad
▴ 10
0
votes
2
replies
223
views
Error in download library file in expression console software
expression
microarray
console
10 hours ago by
Mohammad
• 0
0
votes
6
replies
320
views
Demultiplexing bam file
demultiplexing
bam_file
Iontorrent
1 day ago by
hasani.iut6
▴ 60
1
vote
2
replies
250
views
DEgs RNAseq
RNAseq
2 days ago by
Juan
• 0
0
votes
0
replies
161
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
33 minutes ago by
Vincent Laufer
★ 2.8k
0
votes
1
reply
231
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 2 days ago by
Fabio Marroni
★ 3.0k • written 3 days ago by
1362321710
• 0
1
vote
1
reply
219
views
DownsampleSam
picard
DownsampleSam
updated 3 days ago by
Pierre Lindenbaum
154k • written 3 days ago by
mathalfilip
• 0
0
votes
1
reply
219
views
Error while running Megahit
Megahit
updated 2 days ago by
Mensur Dlakic
★ 23k • written 3 days ago by
abhiramiabhirami9072
• 0
2
votes
5
replies
385
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
13 hours ago by
DanielEB_fisk
• 0
0
votes
0
replies
192
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
4 days ago by
dima
• 0
1
vote
0
replies
247
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics
single-cell
RNA
DEG
4 days ago by
abbas89
▴ 10
0
votes
1
reply
702
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure
pymol
protein
pdb
python
updated 8 hours ago by
Joe
21k • written 4 days ago by
Aatif Hashmi
• 0
0
votes
1
reply
296
views
Deferentially expressed gene with high log2foldchange by DESeq2; but not meaningful at the individual level
DESeq2
RNA-seq
DGEA
updated 4 days ago by
Vincent Laufer
★ 2.8k • written 4 days ago by
Sara
▴ 10
1
vote
2
replies
249
views
Abyss taking a Long time to run
abyss
assembly
genome
fastq
4 days ago by
Maliha
▴ 20
0
votes
2
replies
267
views
Import or read Snapgene .dna files into R
R
.dna
snapgene
4 days ago by
eggrandio
▴ 40
3
votes
4
replies
329
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 10 hours ago by
Joe
21k • written 4 days ago by
antoine.fauchois92
▴ 20
0
votes
0
replies
155
views
BEAST Divergence time Analysis
time
BEAST
BEAUti
divergence
4 days ago by
ahmadjoyyia
▴ 10
0
votes
0
replies
170
views
Differential Gene Expression analysis in heterogeneous tissues
RNA-seq
deseq2
updated 4 days ago by
Ram
39k • written 4 days ago by
txema.heredia
▴ 70
0
votes
1
reply
220
views
Variant Annotation
Variant-Annotation
VCF
R
updated 4 days ago by
Ram
39k • written 4 days ago by
Chethana
• 0
0
votes
1
reply
245
views
too many zeros in 16S rRNA amplicon sequencing data
16S
rRNA
updated 3 days ago by
andres.firrincieli
3.3k • written 4 days ago by
zhangdengwei
▴ 180
0
votes
1
reply
200
views
Finding Kinetic Parameters from Western Blot images
image-processing
western-blot
updated 4 days ago by
Ram
39k • written 4 days ago by
Vijeth
• 0
1,000 results • Page
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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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