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1,000 results • Page 3 of 20
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0
votes
6
replies
364
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq Nanopore ONT differential expression
1 day ago by tw_140 • 0
3
votes
2
replies
189
views
Running STAR on fastq file generated from a RNA-seq experiment
STAR RNAseq fastq files
updated 3 days ago by 4.5k • written 3 days ago by • 0
2
votes
3
replies
293
views
DEseq2 input
DEseq2
updated 3 days ago by 78k • written 3 days ago by ▴ 10
0
votes
1
reply
158
views
Combine Geoids
Geoids NCBI
updated 3 days ago by 78k • written 3 days ago by ▴ 120
1
vote
2
replies
239
views
Best practices for unstranded sequences in featureCounts
featurecounts overlapping unstranded
2 days ago by Enrique • 0
1
vote
1
reply
180
views
Choose between pvalue & pvalue.adj
volcanoplot
updated 3 days ago by 99k • written 3 days ago by • 0
0
votes
5
replies
304
views
HTseq reports missing attribute name
htseq
updated 17 hours ago by 99k • written 3 days ago by • 0
3
votes
0
replies
150
views
Herald: The Biostar Herald for Monday, November 27, 2023
herald
3 days ago by Biostar 2.3k
9
votes
15
replies
761
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
2 days ago by analyst ▴ 10
4
votes
2
replies
1.9k
views
Masurca. Failed to pre-correct Nanopore data, please check your data!
Nanopore Masurca
updated 3 days ago by 5.7k • written 2.4 years ago by ▴ 100
0
votes
0
replies
94
views
Differentiate sequenced and imputed variants in BGEN files
imputation bgen ukb
3 days ago by user230613 ▴ 350
0
votes
4
replies
261
views
Species coverage in the NCBI protein NR database ?
NR
updated 3 days ago by 99k • written 3 days ago by ▴ 10
0
votes
7
replies
421
views
Issues while running htseq-count
Candida-glabrata RNA-seq htseq-count
3 days ago by Foad ▴ 10
0
votes
0
replies
101
views
addPatternDensity to qsea object
maxDensityPattern medip qsea
4 days ago by Jaykishan • 0
1
vote
1
reply
161
views
Harmony integration PC variance explained
scRNA integration harmony
updated 1 day ago by ▴ 20 • written 4 days ago by • 0
0
votes
3
replies
229
views
merged rs number information
merged dbsnp
3 days ago by sskimvd • 0
2
votes
1
reply
152
views
Bedtools intersection
bedtools bed intersect vcf
updated 3 days ago by 158k • written 4 days ago by ▴ 10
0
votes
2
replies
198
views
RnBeads mean difference vs M-values
Methylation
updated 3 days ago by ★ 1.9k • written 4 days ago by ▴ 30
1
vote
2
replies
181
views
RnBeads which p-value to use
Methylation RnBeads
updated 4 days ago by 78k • written 4 days ago by ▴ 30
1
vote
1
reply
163
views
Beginner differential methylation analysis
Methylation
updated 3 days ago by ★ 1.9k • written 4 days ago by ▴ 30
4
votes
8
replies
573
views
Docker: Pass reads file form host to container
docker
3 days ago by davidmaimoun ▴ 50
2
votes
1
reply
236
views
EnhancedVolcano underrepresenting DEGs
R
updated 2 days ago by 86k • written 4 days ago by ▴ 30
4
votes
5
replies
1.7k
views
PyMOL: Gaps in protein structure yet shown by the sequence
PyMOL structure protein
updated 4 days ago by • 0 • written 9 months ago by ▴ 10
0
votes
0
replies
111
views
[maftools]Too many multi_hit and missense mutation
maftools gatk MAF data WES VCF
4 days ago by jiazheng_lin • 0
0
votes
1
reply
180
views
multiple condition and time course in RNA-seq
edgeR RNA-Seq DESeq2
updated 3 days ago by 18k • written 4 days ago by ▴ 30
0
votes
0
replies
124
views
Negative F statistics for sex check in plink
plink check sex
4 days ago by kl ▴ 10
2
votes
4
replies
320
views
Should SMART-seq2 data be deduplicated in STAR?
SMART-seq2
4 days ago by anlinli.napert • 0
0
votes
3
replies
373
views
Extracting list of identical items from several excel files
from excel items Extract file
updated 4 days ago by • 0 • written 5 days ago by ▴ 20
1
vote
2
replies
260
views
Indexing by bowtie2 but aligning with STAR
STAR mm10 Bowtie2 Alignment Index
4 days ago by Anojan • 0
0
votes
1
reply
193
views
Chipseq peak calling and peak frequency region
chipseeker macs2
updated 3 days ago by 3.2k • written 5 days ago by ▴ 10
0
votes
3
replies
318
views
subset a bam file
bam pysam NGS samtools
updated 5 days ago by 136k • written 5 days ago by • 0
1
vote
1
reply
265
views
Forum: want to work in open source project/project in bioinformatics
bioinformatics project
updated 5 days ago by 4.2k • written 5 days ago by • 0
0
votes
0
replies
171
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 days ago by rohitsatyam102 ▴ 780
0
votes
1
reply
247
views
issue in RNA -seq analysis
NGS RNA-Seq
updated 5 days ago by 136k • written 5 days ago by • 0
2
votes
3
replies
1.0k
views
How to identify the 300 kb upstream and downstream genes of lncRNAs?
RNA-Seq lncRNA target genes upstream downstream
updated 6 days ago by • 0 • written 3.0 years ago by ▴ 70
4
votes
6
replies
545
views
BLAST hits on viruses relate to different host than used
Phage BLAST Metagenomics
5 days ago by DonPhager • 0
0
votes
3
replies
341
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA deconvolution Music Music2 bulk
updated 5 days ago by 78k • written 6 days ago by • 0
1
vote
4
replies
423
views
SNPs of a specific mouse strain
snp
updated 5 days ago by 4.2k • written 7 days ago by ▴ 560
0
votes
0
replies
226
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
6 days ago by Wenke • 0
0
votes
3
replies
301
views
Annovar - Annotated file cells show string
annovar
6 days ago by Roshan • 0
2
votes
6
replies
470
views
Genotypes in vcf files
genotypes vcf
updated 6 days ago by 22k • written 6 days ago by ▴ 160
1
vote
1
reply
210
views
Genetic data QC prior to imputation
imputation
updated 6 days ago by ★ 1.3k • written 6 days ago by ▴ 10
4
votes
2
replies
270
views
Excel Pasting Question
Excel
updated 6 days ago by 158k • written 6 days ago by ▴ 10
0
votes
1
reply
242
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW MinION Nanopore
updated 6 days ago by 136k • written 6 days ago by ▴ 40
0
votes
1
reply
214
views
htShinyExample-5.3 - not working
htShiny Oncoprint InteractiveComplexHeatmap
updated 1 day ago by 41k • written 6 days ago by ▴ 60
6
votes
5
replies
3.1k
views
Multi threading bowtie index
bowtie indexing
updated 6 days ago by 5.7k • written 8.2 years ago by ▴ 70
2
votes
4
replies
357
views
Human mitochondrial reference genome
reference genome mitochondria
2 days ago by singhankit973 • 0
0
votes
0
replies
157
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA Worms RNA-Seq
6 days ago by kdca • 0
0
votes
3
replies
273
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
6 days ago by Sara ▴ 230
0
votes
0
replies
879
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics telomeres reads
6 days ago by Mark • 0
1,000 results • Page 3 of 20
Recent Votes
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
Seurat integration of two datasets - GSE126783
about batch correction in scRNA-seq
How to compare two Seurat object (sample) in order to find top markers?
How do I resolve an integration error in Seurat?
The difference between merge and integration with Seurat objects
Analyzing single cell RNA seq with multiple samples and conditions
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Recent Replies
Comment: How can I map coordinates between two strains of yeast? by Jimmy ▴ 10
Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by GenoMax 136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by newbee ▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
Comment: How to get multiple protein domain database domain name from id's by GenoMax 136k
A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
Answer: DIAMOND tutorial by GenoMax 136k
`DIAMOND` has a wiki page: https://github.com/bbuchfink/diamond/wiki Links for DIAMOND papers are here: https://github.com/bbuchfink/diamo…
Comment: How to do simple pathway analysis? by AK ★ 2.2k
Hi [he1k](https://www.biostars.org/u/139817/), Please use the following script which downloads and parses the keg data on the fly: [keg_hi…
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison by CTLong ▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison by CTLong ▴ 20
That's a good point. So its probably safest to not batch correct for within sample comparisons I guess?
Answer: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel by MohammadAlkadi ▴ 70
What is the purpose of doing so? I tried to do that by using the bam file generated by CellRanger. One **important detail** if you are work…
Comment: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data by Kevin Blighe 86k
Thank you - appreciate the translation.
Answer: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data by Kevin Blighe 86k
Em geral, uma taxa de descoberta falsa de 5% (p ajustado<0,05 ) deve ser usada para qualquer teste estatístico em que múltiplas hipóteses i…
Answer: WGCNA tutorial docs needed: Horvath Lab site down by ATpoint 78k
See link here from the developer: https://bioinformatics.stackexchange.com/a/21886/16676
Comment: WGCNA tutorial docs needed: Horvath Lab site down by Katie • 0
I would also appreciate the PDFs if anyone has them please
Answer: Loftee no splice site annotations by AMARU • 0
Hey, did you solve it? I am having a very similar issue. Thanks
Answer: Bulk and Single Cell RNA-seq online course by swbarnes2 13k
I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.
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