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Forum: Contig assembly task, errors
dna contig assembly genetics bioinformatics
updated just now by 8.4k • written 16 minutes ago by • 0
0
votes
1
reply
28
views
bcftools - reducing to "sites-only"?
sites-only bcftools
updated 40 minutes ago by 161k • written 1 hour ago by • 0
0
votes
0
replies
17
views
Enhanced Volcano-Cut off
enhanced foldchange volcano
1 hour ago by odi ▴ 10
0
votes
1
reply
23
views
Help with Biopython for Beginner
Python FASTA Biopython ORF Beginner
updated 30 minutes ago by 161k • written 1 hour ago by • 0
0
votes
0
replies
29
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep vcf gnomad
2 hours ago by asalimih ▴ 60
0
votes
4
replies
263
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
3 hours ago by schmince • 0
0
votes
1
reply
78
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
2 hours ago by Prawesh • 0
795
votes
167
replies
143k
views
109 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 3 months ago by 2.7k • written 7.4 years ago by 100k
0
votes
9
replies
1.4k
views
kinannote software installation problems
kinannote
updated 4 hours ago by • 0 • written 5.7 years ago by ▴ 30
0
votes
1
reply
87
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA hg38 methylation Illumina
updated 4 hours ago by ▴ 90 • written 7 hours ago by ▴ 120
0
votes
0
replies
36
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS WGS Pathway denovo
updated 3 hours ago by 43k • written 6 hours ago by ▴ 90
0
votes
1
reply
177
views
Seurat V5 integration
Seurat integration
updated 3 hours ago by 43k • written 3 days ago by ▴ 10
0
votes
2
replies
139
views
Error in plotting PCA plot in seurat
PCA single-cell seurat scRNA RNA
updated 3 hours ago by 43k • written 17 hours ago by • 0
0
votes
0
replies
52
views
News: Online course: Introduction to Deep Learning
Python Deep-Learning Convolutional-Neural-Network Machine-Learning
updated 3 hours ago by 43k • written 7 hours ago by ★ 2.5k
4
votes
5
replies
3.3k
views
How to compare compare two Sam files to check mapping
alignment
updated 8 hours ago by ▴ 90 • written 6.4 years ago by ▴ 60
0
votes
2
replies
88
views
How/where can I get fungal mitogenome data for analysis?
fungal mitogenome
updated 8 hours ago by 142k • written 9 hours ago by • 0
2
votes
1
reply
147
views
How can I analyze normalized expression data?
DEseq2 RNA-seq
updated 9 hours ago by 5.3k • written 13 hours ago by • 0
3
votes
4
replies
3.9k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 11 hours ago by • 0 • written 5.5 years ago by 8.4k
0
votes
3
replies
174
views
RNA seq analysis
DESeq RNA-seq
updated 4 hours ago by 43k • written 12 hours ago by • 0
10
votes
3
replies
242
views
TFs and Gene databases
Transcription-factor Target Regulatory-Networks
updated 13 hours ago by ▴ 180 • written 1 day ago by • 0
0
votes
0
replies
87
views
Chance for trained without experience
bio
updated 12 hours ago by 82k • written 13 hours ago by • 0
1
vote
2
replies
129
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat Violin-Plot ggplot2 patchwork
13 hours ago by Assa Yeroslaviz ★ 1.8k
0
votes
0
replies
64
views
Xenium multi sample data
batch annotation cell Xenium effect
14 hours ago by Omics data mining ▴ 260
0
votes
2
replies
120
views
Phasing a mixture of two individuals' DNA with long reads
long-reads phasing
12 hours ago by njornet ▴ 20
0
votes
2
replies
138
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect scRNA seurat integration
updated 7 hours ago by ▴ 30 • written 15 hours ago by • 0
0
votes
5
replies
184
views
Percentage coverage of reference genome by de novo genome
SAMtools BWA alignment ddRAD
updated 11 hours ago by 21k • written 15 hours ago by • 0
0
votes
0
replies
83
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2 Hi-C PretextMap
15 hours ago by Winter • 0
0
votes
5
replies
227
views
A question about reference genome for creating the consensus sequence
fasta fa cram genome
9 hours ago by me • 0
2
votes
11
replies
2.6k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 16 hours ago by • 0 • written 4.8 years ago by ▴ 60
2
votes
1
reply
87
views
java out of memory error through beagle for imutation
beagle java.out.of.memory imputation
17 hours ago by analyst ▴ 50
0
votes
0
replies
57
views
Generating .bed file and .map file for polyploid vcf file through plink
bed polyploid map plink
18 hours ago by analyst ▴ 50
0
votes
0
replies
54
views
Blog: Introduction to The Complete Sequence of a Human Genome
biotech
18 hours ago by usa.cd.genomics • 0
0
votes
0
replies
59
views
Blog: Overview of Nanopore Sequencing
biotech
18 hours ago by usa.cd.genomics • 0
0
votes
0
replies
69
views
meffil.snp.concordance
meffil methylation snp_concordance
23 hours ago by kyj222637 • 0
0
votes
1
reply
108
views
PseudobulkExpression.Seurat error
Seurat pseudo-bulk
updated 9 hours ago by 5.3k • written 23 hours ago by ▴ 20
1
vote
5
replies
374
views
HCL database download
HCL
updated 22 hours ago by 43k • written 4 days ago by ▴ 20
0
votes
1
reply
223
views
barcode of TCR-sequencing
barcode
updated 1 day ago by ▴ 60 • written 8 days ago by ▴ 250
0
votes
3
replies
174
views
STAR aligner error
RNA-seq STAR slurm
updated 4 hours ago by 43k • written 1 day ago by ▴ 30
0
votes
0
replies
74
views
monocle 3-- Could not get node in small cluster
monocle3
1 day ago by synat.keam ▴ 100
0
votes
2
replies
164
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression DESeq2
9 hours ago by Nicholas • 0
1
vote
4
replies
326
views
Understanding STAR output (Aligned.out.sam file)
STAR paired-end read
1 day ago by heelpPlease • 0
0
votes
7
replies
410
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 7 hours ago by ★ 2.0k • written 2 days ago by ▴ 140
0
votes
0
replies
94
views
News: Online course. -Time series analysis and Forecasting in R
Time-Series Forecasting R Stastics
1 day ago by carlopecoraro2 ★ 2.5k
0
votes
2
replies
443
views
HLA-HD tool for genomic imputation
genomics imputation bash
updated 1 day ago by • 0 • written 3 months ago by ▴ 10
0
votes
1
reply
156
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort. SAMtools. BAM. SAM.
updated 1 day ago by 142k • written 1 day ago by ▴ 10
5
votes
5
replies
249
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
21 hours ago by Chris ▴ 280
0
votes
2
replies
163
views
Differentail gene expression results
differential expression gene rna-seq Deseq2
updated 7 hours ago by 14k • written 1 day ago by • 0
1
vote
5
replies
194
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 1 day ago by 19k • written 1 day ago by ★ 1.8k
1
vote
1
reply
146
views
student
epitranscriptomics
updated 1 day ago by 82k • written 1 day ago by • 0
0
votes
0
replies
98
views
Imputation of missing genotypes
panel beagle imputation
1 day ago by analyst ▴ 50
116,834 results • Page 1 of 2337
Recent Votes
Difference between Pysam Pileup and Fetch
Answer: Where can I download some example BAM files?
Comment: Where can I download some example BAM files?
Where can I download some example BAM files?
Verify if all the components of a pathway are present in a genomes
removeBatchEffect explained using base R linear models
How to get number of characters (nucleotides) in fasta file
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Recent Replies
Answer: Contig assembly task, errors by Philipp Bayer 8.4k
Feels a bit strange for an aptitude test, feels more like homework. 1) seems OK to me, just chuck them into CAP3 and see what falls out.…
Comment: Help with Biopython for Beginner by Pierre Lindenbaum 161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: bcftools - reducing to "sites-only"? by Pierre Lindenbaum 161k
bcftools view -G in.vcf.gz <!-- Diabetic foot ulceration (DFU) is a devastating complication of diabetes whose pathogenesis rema…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
I probably got some of the vocabulary wrong. I thought that "Dom HOR2932 HOR3036 HOR3726 KWSBambina Rec S42IL_124" were representing my ge…
Comment: featureCounts output assigned value higher than and HISAT2 mapping. by Ram 43k
It's featureCount**s**, not featureCount. I've edited your post and fixed all mentions of featureCounts.
Comment: kinannote software installation problems by Emanoelle • 0
Hey, I know it's been 5 years but I have the same issue. When I run the test the software is unable to perform and always deliver the follo…
Comment: STAR aligner error by Ram 43k
If they can't help you, we probably can't do much either. But we can optimize your STAR command. BAM SortedByCoordinate is the worst settin…
Answer: Obtaining Infinium Methylation450K manifest for hg38 by marco.barr ▴ 90
Hi, you can check it from github here: [https://zwdzwd.github.io/InfiniumAnnotation][1]. I don't know if this is what you are looking fo…
Comment: RNA seq analysis by ATpoint 82k
It makes absolutely no sense to conduct such an analysis. I strongly discourage you to even start with it. Results will be utterly nonsense…
Comment: Differentail gene expression results by swbarnes2 14k
Cross-posted: https://support.bioconductor.org/p/9158194/
Answer: Seurat V5 integration by Bastien Hervé 5.3k
It will depend on your context and question. I guess you will want to compare gene expression between your conditions within cell types …
Answer: Error in plotting PCA plot in seurat by Adam ▴ 30
You get this error when you try to compare two data frames that have different dimensions. Try using the traceback() command to figure out …
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
Sorry, this was supposed to be a comment appended to the chain above. I didn't mean to post as an answer.
Comment: Exploring Diet Effects in Single-Cell RNA Sequencing by Adam ▴ 30
> when I looked at the expression of aging marker genes, I noticed that diets sequenced in the same batch appeared more similar. How simil…
Answer: How to compare compare two Sam files to check mapping by DavidStreid ▴ 90
Curious if others have also benefited from Picard's [CompareSAMs][1] tool. Seems to do exactly what Madhu has requested. If the headers …
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