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122,201 results • Page 667 of 2445
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Clustering 10X scRNA data based on selected markers
clustering scRNA seurat umap pca
4.6 years ago by A • 0
0
votes
0
replies
651
views
KeyError in the pipeline SECAPR
SECAPR Hyb-Seq locus_selection Python Key_error
4.6 years ago by Begonia_pavonina ▴ 210
2
votes
1
reply
674
views
Compatilibity between human37 and human38 gtf
GRCh37v75
updated 4.6 years ago by 48k • written 4.6 years ago by ▴ 70
0
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0
replies
3.0k
views
Question about FindMarkers avg_logFC and how to get all features from an assay
seurat singlecell Seurat
4.6 years ago by compuTE ▴ 140
8
votes
8
replies
2.7k
views
6 follow
DESeq2 adjusted p-values of 0 when p-value > 0.05
RNA-seq DEseq2
updated 4.6 years ago by ▴ 390 • written 4.6 years ago by • 0
0
votes
0
replies
601
views
How to calculate the weighted average for each linkage group?
QTLMapping Genetics
4.6 years ago by wkmustahs21 ▴ 30
1
vote
4
replies
2.5k
views
Prefetch not working for SRA
SRA prefetch
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
0
replies
683
views
Job: Evolutionary and anthropological genomics postdoctoral fellow at University at Buffalo
Evolution Anthropology Transcriptomics Genomics
4.6 years ago by Omer • 0
0
votes
3
replies
1.3k
views
Gene filtering returns NULL dimensions
R filtering affymetrix genefilter CEL
4.6 years ago by purestdata • 0
0
votes
4
replies
1.4k
views
Very low alignment rate for miRNAs reads against known miRNAs from mirbase
smRNA
updated 4.6 years ago by 23k • written 4.6 years ago by • 0
1
vote
5
replies
1.8k
views
How to ID cell types using reference scRNAseq dataset
Seurat groups scRNAseq
4.6 years ago by FantasticAI ▴ 60
3
votes
1
reply
833
views
Criteria for classifying circular sequences
genome GenBank circular sequence
updated 4.6 years ago by ★ 30k • written 4.6 years ago by ▴ 10
1
vote
1
reply
891
views
How to overcome issue linked to loading big R object
R methylation bioconductor minfi
4.6 years ago by Fede_Santos95 ▴ 20
0
votes
2
replies
1.3k
views
Make info tag separate column VCF
vcf ANGSD
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 20
3
votes
1
reply
6.9k
views
When use enricher function or GSEA of clusterProfiler R
GSEA enricher genes enrichment clusterProfiler
updated 4.6 years ago by 35k • written 4.6 years ago by ▴ 20
1
vote
4
replies
1.7k
views
Blast Output with only one line
blast
4.6 years ago by pablo ▴ 350
1
vote
3
replies
1.5k
views
Use BCBio package
windows Python3.9
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 80
2
votes
3
replies
1.4k
views
Mitochondrial genes filtration
scRNA-Seq
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
3
replies
3.8k
views
Where to get genetic map build 38 ?
genome next-gen
updated 4.6 years ago by • 0 • written 7.5 years ago by ▴ 350
3
votes
8
replies
2.2k
views
how to order values with different classes in R
R order
4.6 years ago by szp770 ▴ 10
1
vote
2
replies
1.3k
views
Getting Null in sink file when running lme in R using python to generate multiple R codes
R python lme sink
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 70
0
votes
0
replies
684
views
GATK VariantEval no concordance between dbSNP and our data
VariantEval GATK dbSNP Percentage
4.6 years ago by Pierre_Bioinfo • 0
5
votes
3
replies
1.5k
views
Where I can get the gtf file of antheraea mylitta
GTF
updated 4.6 years ago by 16k • written 4.6 years ago by ▴ 80
0
votes
4
replies
1.4k
views
How to merge genomic features shared by more than one samples
bedtools gene RNA-seq bed annotation
4.6 years ago by tianshenbio ▴ 190
0
votes
5
replies
2.6k
views
substance BxH
WGCNA
updated 4.6 years ago by ★ 90k • written 4.6 years ago by • 0
0
votes
0
replies
805
views
Tool for list protein mutation sites from WT/variants sequences
Mutations Protein
updated 2.5 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
870
views
Extracting the genes associated drugs?
bank Drug
4.6 years ago by mathavanbioinfo ▴ 80
2
votes
2
replies
1.3k
views
Remove all rows that begin with characters and keep only those that begin with numbers in Linux.
hg19 linux
updated 4.6 years ago by 36k • written 4.6 years ago by ▴ 70
0
votes
2
replies
1.6k
views
Variant Calling with Vartrix: Warning with VCF and Error with FASTA
vcf vartrix fasta
4.6 years ago by d • 0
0
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0
replies
1.0k
views
DiffBind3 outputs compared to previous versions
DiffBind3 R ChIP-seq EdgeR Deseq2
4.6 years ago by gkunz ▴ 30
138
votes
19
replies
201k
views
13 follow
What'S The Difference Between Cds And Orf?
cds orf
updated 4.6 years ago by • 0 • written 13.5 years ago by ▴ 380
1
vote
0
replies
960
views
Job: Computational Biology Lab Head, Brain Cancer Centre, Melbourne, Australia
cancer wehi australia
4.6 years ago by Gordon Smyth ★ 8.6k
5
votes
4
replies
1.4k
views
BWA-mem alignment
WGS Data Genomics
updated 4.6 years ago by 90k • written 4.6 years ago by ▴ 20
0
votes
3
replies
1.3k
views
Obtaining required rows from HG19 file with R or Linux
hg19
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 70
101
votes
19
replies
39k
views
19 follow
Tutorial: Heatmaps in R
heatmap R
updated 13 months ago by ▴ 70 • written 9.3 years ago by 27k
0
votes
1
reply
1.3k
views
Position of Scale bar
ggplot2
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Forum: Phylogenomic study: suggestions and tips
evolution species genus phylogenomic phylogenetics
4.6 years ago by tiagobellintani ▴ 40
2
votes
2
replies
1.4k
views
paired reads have different names
BWA
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Predicting Drug responds from somatic mutations
prediction somatic responds drug
updated 4.6 years ago by ▴ 590 • written 4.6 years ago by ▴ 420
5
votes
9
replies
13k
views
6 follow
ANOVA for RNA-seq data?
anova RNA-Seq
updated 4.2 years ago by 9.0k • written 6.0 years ago by ▴ 120
0
votes
2
replies
2.1k
views
Batch effects and differential expression analysis on TCGA data for cancer subtypes
RNA-Seq TCGA batch
4.6 years ago by antmantras ▴ 80
7
votes
6
replies
7.9k
views
How to create SAF from text file for FeatureCounts
featureCounts ATAC-seq
updated 16 months ago by ▴ 80 • written 4.6 years ago by ▴ 70
0
votes
1
reply
1.1k
views
update fasta header and gff3 file
fasta gff awk header python
updated 4.6 years ago by ★ 1.3k • written 4.6 years ago by ▴ 10
0
votes
1
reply
2.4k
views
Greengenes homepage
Greengenes
updated 4.6 years ago by 35k • written 4.6 years ago by ▴ 340
2
votes
5
replies
2.0k
views
Use Rfam to remove contaminants from miRNA-seq
Rfam miRNA contaminant sequensing
updated 4.6 years ago by 22k • written 4.6 years ago by ▴ 20
0
votes
0
replies
1.1k
views
dynamic input/output in the snakemake rules
RNAseq Snakemake dynamic bam
4.6 years ago by ali • 0
2
votes
2
replies
1.7k
views
SNP count in a set of genomic regions
annotations SNPs 1000G
updated 4.6 years ago by 14k • written 4.6 years ago by ▴ 90
50
votes
17
replies
42k
views
17 follow
How To Get Number Of Reads In Bam File Efficiently In Python?
python samtools next-gen sequencing
updated 3.1 years ago by 45k • written 15.3 years ago by ▴ 840
0
votes
0
replies
749
views
average variants number human WGS
variant WGS SNP INDEL
4.6 years ago by cocchi.e89 ▴ 300
1
vote
1
reply
1.4k
views
two allele frequency
allele position BCFTOOLS
updated 4.6 years ago by 14k • written 4.6 years ago by ▴ 110
122,201 results • Page 667 of 2445
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strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
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