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1,000 results • Page 6 of 20
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2
votes
3
replies
319
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 11 days ago by ★ 2.0k • written 12 days ago by ▴ 30
0
votes
0
replies
159
views
SIngle cell analysis
Seurat scRNA-seq Harmony DoubletFinder Merge
12 days ago by Jeyong • 0
0
votes
2
replies
741
views
homer not configured properly
Homer makeTagDirectory
updated 12 days ago by • 0 • written 24 months ago by • 0
1
vote
3
replies
298
views
Bedtools merge minimum overlap?
bedtools genomics
updated 12 days ago by 35k • written 12 days ago by • 0
0
votes
0
replies
145
views
Empty table plot using plotGseaTable()
FGSEA
11 days ago by Chris ▴ 280
0
votes
1
reply
205
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 12 days ago by ▴ 120 • written 12 days ago by • 0
1
vote
3
replies
260
views
DiffBind: no peaks in DBA
MACS2 DiffBind ChIP-seq
updated 12 days ago by ★ 16k • written 12 days ago by ▴ 10
3
votes
5
replies
371
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
11 days ago by Maverick ▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 12 days ago by • 0 • written 5.1 years ago by 11k
0
votes
2
replies
224
views
Base Quality Score Recalibration with different reference genome
SNPs GATK BQSR RNA-seq
12 days ago by dtnondorf • 0
3
votes
8
replies
672
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 8 days ago by ▴ 410 • written 12 days ago by ▴ 100
1
vote
2
replies
267
views
RNA-seq data for deep learning classification
rna-seq
12 days ago by yahn • 0
3
votes
8
replies
567
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
8 days ago by Qroid ▴ 40
0
votes
1
reply
531
views
Loss of 'var' using concatenation of AnnData objects
Scanpy AnnData
updated 12 days ago by • 0 • written 5 months ago by • 0
0
votes
1
reply
172
views
Provean help
variant Provean
updated 12 days ago by ★ 27k • written 12 days ago by • 0
1
vote
1
reply
179
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL GTEx
updated 12 days ago by ★ 2.4k • written 13 days ago by ▴ 20
1
vote
1
reply
187
views
Super ehancers
enhancers
updated 12 days ago by ★ 16k • written 13 days ago by • 0
4
votes
7
replies
387
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
1 day ago by Chen • 0
5
votes
5
replies
308
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 12 days ago by ▴ 30 • written 13 days ago by ▴ 150
1
vote
7
replies
481
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
12 days ago by eebloom ▴ 80
3
votes
3
replies
358
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression RNA NOISeq DGE
updated 12 days ago by 82k • written 13 days ago by • 0
0
votes
0
replies
104
views
Use of annotation of integrated Seurat object in single sample
Seurat
13 days ago by Bine ▴ 60
0
votes
0
replies
114
views
News: Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding Programming R
updated 12 days ago by 43k • written 13 days ago by ★ 2.5k
0
votes
1
reply
248
views
Subsetting and merging back Seurat Object brings different results
Seurat
12 days ago by Bine ▴ 60
0
votes
0
replies
170
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS Genomics Post-doc R-loops
updated 12 days ago by 43k • written 13 days ago by • 0
1
vote
1
reply
156
views
Discrepancy in read counts from fastq
downsampling fastq
updated 12 days ago by 43k • written 13 days ago by ▴ 110
0
votes
0
replies
105
views
Successfully identified and Masked rpeats using RM. What Next?
sequence annotation repeatmasker illumina assembly
13 days ago by Vijith ▴ 30
10
votes
14
replies
727
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 7 days ago by 142k • written 13 days ago by • 0
0
votes
1
reply
292
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 13 days ago by ▴ 280 • written 19 days ago by • 0
0
votes
0
replies
107
views
Combining Methylation Microarray data from different platforms
Microarray DNA EPIC 450K Methylation
13 days ago by James ▴ 10
0
votes
1
reply
600
views
Basic stats in hierfstat
Fst stats hierfstat
updated 13 days ago by • 0 • written 19 months ago by • 0
1
vote
3
replies
272
views
Odd alignment question/finding
Alignment
updated 12 days ago by ★ 2.1k • written 13 days ago by • 0
0
votes
1
reply
222
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK recalibration
updated 13 days ago by 142k • written 13 days ago by ▴ 30
0
votes
0
replies
132
views
Looking for the best way to interpret these data
RNA-seq ontology GO
updated 13 days ago by 43k • written 13 days ago by ▴ 10
0
votes
7
replies
612
views
Post-imputation plot
michigan-imputation-server quality-control
updated 12 days ago by 3.9k • written 15 days ago by ▴ 10
0
votes
1
reply
239
views
How to find overlap of clusters in two seurat porject
clustering seurat
updated 13 days ago by ▴ 30 • written 14 days ago by • 0
1
vote
3
replies
343
views
DESeq2 processing problems
deseq2 R
updated 13 days ago by 82k • written 14 days ago by • 0
0
votes
1
reply
794
views
cnetplot category names are too long
clusterprofiler RNA-Seq enrichplot cnetplot
updated 12 days ago by 43k • written 2.7 years ago by • 0
0
votes
1
reply
169
views
Mutect2 for mitochondria variant discovery
mutect2 mitochondria
updated 13 days ago by 43k • written 13 days ago by • 0
0
votes
0
replies
114
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent bacteria circularise
13 days ago by VITALA • 0
1
vote
2
replies
281
views
POSSUM not working due to incompatible pssm file
fasta pse-pssm pssm POSSUM
13 days ago by rianna.collins • 0
0
votes
1
reply
198
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 14 days ago by 19k • written 14 days ago by • 0
0
votes
0
replies
157
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics metacyc enzyme pathway genomics
14 days ago by O.rka ▴ 720
0
votes
1
reply
697
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 14 days ago by 43k • written 14 days ago by • 0
2
votes
2
replies
302
views
p-value in CIBERSORT
CIBERSORT p-value
14 days ago by michelafrancesconi9 ▴ 20
0
votes
5
replies
414
views
Telescope issue
Telescope RNA-seq
updated 13 days ago by 142k • written 14 days ago by • 0
5
votes
6
replies
578
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 14 days ago by ▴ 760 • written 15 days ago by ▴ 40
1
vote
1
reply
250
views
Adjust pvalue in R with different approach give me all different outcome
statistics R p-value
updated 14 days ago by 43k • written 14 days ago by ▴ 60
1
vote
2
replies
316
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast pssm
14 days ago by Nafi • 0
1
vote
3
replies
316
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA illumina GEO metadata
updated 14 days ago by 142k • written 14 days ago by • 0
1,000 results • Page 6 of 20
Recent Votes
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
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Comment: bbmerge (bbmap) ~ error with insert size file output by GenoMax 142k
> It is confirmed (and solved in another thread) that we have significant overlapping paired end reads. Can you provide a reference to sai…
Comment: Duplicated reads (IDs) from nanopore sequencing by GenoMax 142k
> I get the exact same read with the same ID and all more than once If you have short(er) reads you could be seeing secondary alignments. …
Answer: Duplicated reads (IDs) from nanopore sequencing by marco.barr ▴ 110
Hi, I'm also working with ONT data and with dorado. From experience I tell you that some versions of MInKNOW have bad management of fast5 f…
Comment: Problem with Calling Variants from RNA-Seq data by Esraa • 0
Yes, i specifically ran the RNA-seq best practices, and no i have not taken RNA editing into account considering this is not mentioned in t…
Comment: Problem with Calling Variants from RNA-Seq data by i.sudbery 19k
Have you accounted for A>I RNA editing?
Comment: Problem with Calling Variants from RNA-Seq data by Esraa • 0
**My references** Genome: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_al…
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p by ATpoint 82k
This has formally been investiated by a reputable group here: https://academic.oup.com/nar/article/42/11/e95/1442937 IIRC they think tha…
Comment: RNA seq analysis by Jacek ▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap by dariober 14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python by JACKY ▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by melissa.joubert • 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
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