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1,000 results • Page
3 of 20
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0
votes
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199
views
OMA in AWS cloud
OMA
AWS
updated 5 days ago by
Ram
40k • written 5 days ago by
Ksel
• 0
0
votes
5
replies
433
views
genome data downloads for various strains
gisaid
hass-marr
updated 1 day ago by
Ram
40k • written 5 days ago by
iftikharmaryam123
• 0
0
votes
0
replies
180
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
5 days ago by
juliviglino
• 0
3
votes
2
replies
326
views
Identifying common DEGs among multiple datasets
R
DEG
updated 5 days ago by
Barry Digby
★ 1.2k • written 6 days ago by
Shma
• 0
4
votes
8
replies
562
views
Assistance with Fungal Genome Annotation Using Maker and BLAST
gff3
fasta
maker
xml
blastp
1 day ago by
Edoardo
• 0
0
votes
0
replies
160
views
News:
Workshop - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)
workshop
scRNA-Seq
RNA-Seq
single-cell
updated 5 days ago by
Ram
40k • written 5 days ago by
David Langenberger
10k
3
votes
3
replies
355
views
Forum:
Importance of Data Structures for Bioinformatics?
data-structures
updated 5 days ago by
Ram
40k • written 6 days ago by
S
• 0
0
votes
2
replies
272
views
How to find positions with higher depth relative to their surroundings
depth
python
samtools
updated 5 days ago by
xiaoguang
▴ 130 • written 6 days ago by
hyperdx1
• 0
0
votes
0
replies
155
views
News:
Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
sequence-analysis
sars-cov-2
spike-protein
updated 5 days ago by
Ram
40k • written 5 days ago by
Prem
• 0
3
votes
2
replies
265
views
How to retrieve LoF and missense variants in WES data?
bcftools
variants
plink
SNPs
updated 5 days ago by
luffy
▴ 40 • written 6 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
363
views
Recommended workflow for identifying the genomic location and copy-number of an insert with a known sequence from WGS Nanopore fastq files
Nanopore
WGS
Long-Read
updated 5 days ago by
Ram
40k • written 6 days ago by
dk0319
▴ 70
3
votes
1
reply
190
views
What is the difference between norm --multiallelics -any versus --atomize?
bcftools
updated 6 days ago by
Ram
40k • written 6 days ago by
a615ebfb
▴ 30
4
votes
0
replies
194
views
Herald:
The Biostar Herald for Wednesday, September 20, 2023
herald
6 days ago by
Biostar
2.0k
1
vote
4
replies
306
views
I need to retrieve a set of protein and mRNA sequences
Protein
mRNA
sequences
updated 6 days ago by
Ram
40k • written 6 days ago by
george
• 0
0
votes
1
reply
202
views
Esearch, Epost, and Efetch for Large Datasets in Biopython
eutils
biopython
entrez
updated 5 days ago by
Ram
40k • written 6 days ago by
Salem
• 0
1
vote
2
replies
239
views
GSEA Result Visualization in R
r
enrichplot
gsea
visualization
enrichResult
6 days ago by
Cortney
• 0
1
vote
2
replies
263
views
How to separate proteins on the same chain?
pdb
protein
updated 5 days ago by
Ram
40k • written 6 days ago by
Zayyan
▴ 10
0
votes
2
replies
228
views
how to evaluate SNPs that are regulating same gene expression across multiple tissues
snp
GTEx
updated 6 days ago by
LChart
3.4k • written 6 days ago by
rheab1230
▴ 140
3
votes
10
replies
500
views
STAR index not working
STAR
RNA-Seq
5 days ago by
camillab.
▴ 130
1
vote
2
replies
376
views
How to display all top markers in the heatmap by DoHeatmap (Seurat) when there are duplicates of top marker genes for several cell clusters
DoHeatmap
Seurat
6 days ago by
alwayshope
▴ 30
2
votes
3
replies
279
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication
apoptosis
updated 6 days ago by
Ram
40k • written 6 days ago by
txema.heredia
▴ 80
0
votes
1
reply
163
views
Prank checkpoint and restore?
prank
alignment
updated 6 days ago by
Ram
40k • written 6 days ago by
Pit
• 0
0
votes
0
replies
739
views
Job:
Research Scientist 5 – Bioinformatics and Computer Biology, Center for Dementia Research (CDR), Nathan Kline Institute for Psychiatric Research
Neuroscience
Biostatistics
updated 6 days ago by
Ram
40k • written 6 days ago by
cdrinfo
• 0
0
votes
1
reply
183
views
gffread outputs empty gtf file
gff
gffread
gtf
updated 6 days ago by
inedraylig
▴ 20 • written 6 days ago by
sumitra.20
• 0
0
votes
13
replies
560
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
3 days ago by
Y
• 0
5
votes
7
replies
475
views
Elusive syntax error in Snakefile
snakemake
updated 6 days ago by
Ram
40k • written 7 days ago by
Giuseppe Giovanni
▴ 30
1
vote
3
replies
242
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools
guppy
updated 6 days ago by
GenoMax
134k • written 6 days ago by
anika.john
• 0
8
votes
10
replies
720
views
Inflated GWAS test statistic after merging multiple batches of genotype dataset imputed differently
genotype
imputation
gwas
updated 6 days ago by
LauferVA
3.7k • written 7 days ago by
Amy
▴ 20
0
votes
13
replies
662
views
Dealing with transcriptome sequences that are smaller than their respective genes
blastn
Trinity
Transcriptome
RNA-seq-analysis
De-novo-transcriptome-assembly
4 days ago by
langziv
▴ 50
2
votes
2
replies
208
views
Kraken2 recovering only classified reads
Kraken2
taxonomy
classification
6 days ago by
SushiRoll
▴ 110
0
votes
0
replies
117
views
Any way to predict hormone biosynthesis pathways in understudied organisms?
genomics
orthologs
biosynthesis-pathway
updated 6 days ago by
Ram
40k • written 6 days ago by
Mark
• 0
2
votes
4
replies
314
views
Refseq annotation | Populus trichocarpa
R
RNA-seq
plants
Refseq
updated 6 days ago by
Ram
40k • written 6 days ago by
P
• 0
1
vote
1
reply
197
views
Read Counts from BAM file
bam
samtools
qualimap
readcount
updated 6 days ago by
ATpoint
76k • written 6 days ago by
Smriti
• 0
10
votes
8
replies
576
views
Adding a control sample to bulk RNA-seq
RNA-seq
5 days ago by
Chris
▴ 180
19
votes
14
replies
876
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 6 days ago by
Jeremy Leipzig
21k • written 7 days ago by
vincenthus
▴ 70
0
votes
2
replies
235
views
Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data?
scrna-seq
rna-seq
log2fc
6 days ago by
JLee
• 0
1
vote
3
replies
334
views
VDJ reconstitution from 3' 10x genomics platforms
VDJ
updated 7 days ago by
Ram
40k • written 7 days ago by
gal.dadi
• 0
0
votes
1
reply
190
views
Identify parent of each read in a GAF
gaf
vgteam
vg
updated 7 days ago by
Jordan M Eizenga
▴ 360 • written 7 days ago by
cfourps
▴ 10
0
votes
3
replies
253
views
Errors while trying to run Scenic
Scenic
updated 7 days ago by
GenoMax
134k • written 7 days ago by
Stavroula
• 0
0
votes
3
replies
267
views
How to find target genes From RNA seq data?
Cotton
DGE
RNA-seq
updated 7 days ago by
Ram
40k • written 7 days ago by
Fizzah
▴ 30
1
vote
2
replies
221
views
STAR error EXITING because of FATAL ERROR: failed reading from temporary file
STAR
RNA-seq
updated 7 days ago by
GenoMax
134k • written 7 days ago by
erik.burchard
▴ 20
2
votes
3
replies
269
views
Is there an easy to modify the subplot titles in DimPlot (Seurat)?
scRNA-seq
patchwork
DimPlot
Seurat
updated 6 days ago by
Nicolas Rosewick
10k • written 7 days ago by
alwayshope
▴ 30
0
votes
0
replies
134
views
News:
Course: Data Manipulation and Visualisation with Python
Python
Data-Visualization
Data-Manipulation
updated 7 days ago by
Ram
40k • written 7 days ago by
carlopecoraro2
★ 2.3k
0
votes
1
reply
242
views
VCF QUAL field for multiple samples
variants
VCF
updated 7 days ago by
DBScan
▴ 180 • written 15 days ago by
Ron
• 0
0
votes
3
replies
498
views
CNV calling
CNV
NGS
Variant-Calling
updated 6 days ago by
Zhenyu Zhang
▴ 980 • written 8 months ago by
adarsh_pp
▴ 30
2
votes
1
reply
229
views
bedGraphToBigWig: Missing Genome Coordinates
bamtobed
bed
7 days ago by
vanbelj
▴ 40
0
votes
0
replies
136
views
maftools - median survival time doesn't match plot
R
survival
maftools
K-M
7 days ago by
BioGuy
• 0
6
votes
8
replies
517
views
Find potential important genes from bulk-RNA seq experiment
RNA-seq
4 days ago by
Chris
▴ 180
0
votes
1
reply
170
views
vg rna pantranscriptome
rna
vg
updated 7 days ago by
Jordan M Eizenga
▴ 360 • written 7 days ago by
z
• 0
0
votes
0
replies
126
views
Genetic distance in cM from VCF of non-reference species to run Beagle
plink
beagle
vcf
updated 7 days ago by
Ram
40k • written 7 days ago by
AndrMod
• 0
1,000 results • Page
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Recent Votes
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
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Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Answer: Fetch Fastq files directly for SRA data
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6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe
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Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject
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Jordan M Eizenga
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This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis?
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Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
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Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject
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It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis?
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Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
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Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question
by
Istvan Albert
98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate
by
dsull
★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
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morovatunc
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Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
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> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
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by
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• 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
Comment: Violin plot (Monocle 3) - Troubleshooting
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The error message tells me there is the possibility of a conflicting function called `plot_genes_violin` that accepts one parameter and err…
Comment: Violin plot (Monocle 3) - Troubleshooting
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★ 1.2k
I m not sure why you have problem there. I do not encounter any problem. May be your gene list are not present in your source object. Pleas…
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