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122,202 results • Page 681 of 2445
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2.0k
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How to Estimate total variance in, and between RNA-seq datasets?
batch variance correction
4.6 years ago by Gabriel ▴ 180
1
vote
1
reply
1.0k
views
Detection of bacterial SNP using regular PCR primers
detection PCR SNP
updated 4.6 years ago by ▴ 170 • written 4.6 years ago by ▴ 180
3
votes
4
replies
6.7k
views
Can't change coefficient of dds object: error 'coef' should specify same coefficient as in results 'res'
DESeq2 RNA-seq
4.6 years ago by macielrodriguez2 ▴ 50
3
votes
2
replies
1.7k
views
How can I revert back the Ensembl vep annotated positions to vcf positions?
ensembl VEP VCF
updated 4.6 years ago by 90k • written 4.6 years ago by ★ 4.5k
0
votes
0
replies
895
views
Negative branch length when using clustalw through Python and unable to see bootstrap values
clustalw Phylogeny bootstrap Python tree
4.6 years ago by minifoog ▴ 10
1
vote
3
replies
2.7k
views
About combining the forward and reverse sequence
16srRNA geneious
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
0
replies
879
views
<*> meaning in Vcf Output From Mpileup
mpileup missing deletion vcf
4.6 years ago by breezin • 0
4
votes
6
replies
8.4k
views
Fastqc shows over-represented sequence with no sequence given?
sequencing
updated 3.0 years ago by 45k • written 10.4 years ago by ▴ 50
5
votes
3
replies
4.5k
views
how remove large gene ontology terms from gprofiler2 output
gprofiler2 GO DEseq RNA-seq
updated 4.6 years ago by ★ 19k • written 4.6 years ago by ▴ 10
0
votes
0
replies
1.9k
views
Job: R/Shiny web application developer in bioinformatics startup
web visualization shiny
4.6 years ago by ivo.kwee • 0
0
votes
2
replies
3.4k
views
freebayes for snp call in pooled samples: how do I set the parameters?
SNP freebayes pooled ploidy
updated 4.6 years ago by ▴ 10 • written 5.7 years ago by • 0
2
votes
6
replies
2.8k
views
Can't count features with featurecount
RNAseq featurecounts
4.6 years ago by avelarbio46 ▴ 30
1
vote
3
replies
789
views
How do I find the gene name with the allele number from the databases?
rna-seq
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
1
vote
2
replies
1.9k
views
How to implement k fold cv after randomForest
k_fold_cv R randomForest
4.6 years ago by pt.taklifi ▴ 70
4
votes
2
replies
5.2k
views
How to visualize Multiple Sequence Alignment with python ?
python clustalw msa
updated 4.6 years ago by ★ 30k • written 4.6 years ago by • 0
0
votes
0
replies
967
views
Is there a faster way to download gene sequences from NCBI via E-utils
NCBI E-utils Unix
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 60
0
votes
0
replies
775
views
Job: Postdoc Fellow @ New York City: Alternative Splicing
splicing genomics rnaseq
4.6 years ago by fanggang ▴ 120
2
votes
4
replies
1.9k
views
Finding how many times a nucleotide appear in the same position
Beginer Nucleotide Python DNA
updated 4.6 years ago by 166k • written 4.6 years ago by • 0
1
vote
2
replies
1.5k
views
Taxonomy assignment of viral RNA
assembly taxa metagenomics
4.6 years ago by biobiu ▴ 150
7
votes
12
replies
3.9k
views
RNAseq data analysis of pooled data
DESeq2 mapping featurecounts clustering RNA-Seq
updated 4.6 years ago by ★ 2.6k • written 4.6 years ago by ▴ 130
0
votes
0
replies
766
views
Identify sample mix from NGS data
NGS samplemix contamination celllineauthentication
4.6 years ago by Boberoni ▴ 20
2
votes
1
reply
1.2k
views
CNV-calling single sample
copynumbervariation cnv GATK na12878
updated 22 months ago by ▴ 200 • written 4.6 years ago by ▴ 20
0
votes
0
replies
2.1k
views
Is there any Python or other software that can replace the function "networklevel" in R package "bipartite" for calculation?
R networklevel
4.6 years ago by 153348734 • 0
2
votes
3
replies
1.6k
views
GTF file and Transcript ID
transcriptid rnaseq gtf
updated 4.6 years ago by ★ 2.2k • written 4.6 years ago by ▴ 10
0
votes
1
reply
887
views
Couldnot access BSRD database
database website BSRD
updated 16 months ago by • 0 • written 4.6 years ago by • 0
0
votes
0
replies
892
views
CPM or TPM values as discretization method input
RNA-Seq discretization TPM CPM
4.6 years ago by antmantras ▴ 80
3
votes
4
replies
3.0k
views
Expression of gene of interest across conditions in single-cell data
singlecell scater tpm seurat Rna-seq
4.6 years ago by kz • 0
0
votes
1
reply
1.6k
views
bbmap, mapq and uniquelly mapped reads filtering
alignment mapq
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 880
0
votes
3
replies
1.8k
views
Cell composition in each condition of single cell data
cell composition single-cell scProportionTest
4.6 years ago by paria ▴ 110
2
votes
6
replies
2.7k
views
Generate a file with SNPs given a WGS dataset
annotation snp ngs
4.6 years ago by iibrams07 ▴ 10
0
votes
0
replies
704
views
Calculate relative position of one range with respect to another
Bioconductor IRanges GenomicRanges R
4.6 years ago by Andrew • 0
0
votes
5
replies
2.6k
views
Limma experiment design and making contrasts
limma methylation 450k
4.6 years ago by kra277 • 0
6
votes
4
replies
4.3k
views
Keep values from VCF file into Ensembl VEP annotation
SNP
updated 3.8 years ago by ▴ 60 • written 4.9 years ago by ▴ 840
4
votes
6
replies
2.4k
views
Using outgroup in gene family dendograms
mega dendograms
4.6 years ago by Rogerio Ribeiro ▴ 110
0
votes
0
replies
2.1k
views
I can not get fasta file with the hit sequences running barrnap
barrnap bed
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 50
0
votes
1
reply
903
views
Raw read processing using trimmomatic
trimmomatic
updated 4.6 years ago by ▴ 880 • written 4.6 years ago by ▴ 10
2
votes
3
replies
2.0k
views
How to extract only the specific fasta sequences by matching the ID's to a different source files ?
RNA alignment DNA
updated 4.6 years ago by ★ 2.2k • written 4.6 years ago by ▴ 210
2
votes
2
replies
1.5k
views
Download discontinued gene record from NCBI via E-utils
E-utils NCBI Discondinued Gene
4.6 years ago by lmlukoseviciute ▴ 60
4
votes
6
replies
4.4k
views
Creating reference genome for mapping and then selecting
mm10 hg38 STAR RNA-seq
updated 4.6 years ago by 103k • written 4.6 years ago by ★ 2.8k
0
votes
2
replies
2.8k
views
ExomeDepth negative BF (bayesian factor) values meaning
WES DNA-seq CNV
updated 4.6 years ago by ★ 3.0k • written 4.8 years ago by ▴ 160
3
votes
2
replies
1.4k
views
Tool to find chromosome specific repeats
FISH repeats transposons genomics
updated 4.6 years ago by 56k • written 4.6 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Different results in limma if group is removed
limma edgeR
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 140
0
votes
2
replies
1.5k
views
LOOCV on limma results
loocv limma cross-validation
4.5 years ago by Palgrave ▴ 140
0
votes
0
replies
670
views
mtDNA variant calling
variant fasta seq mtdna
4.6 years ago by here_for_learning • 0
1
vote
4
replies
2.4k
views
How do I compare degree and betweenness centrality for different PPI networks?
PPI centrality degree Cytoscape network
4.6 years ago by gemmalouisebaldock ▴ 20
0
votes
5
replies
2.3k
views
What Coverage allele-fraction threshold to use?
allele-fraction snps
updated 2.2 years ago by 45k • written 4.6 years ago by ▴ 180
0
votes
2
replies
1.1k
views
Extracting transcripts from whole-transcriptome libraries
galaxy vcf rna-seq
4.6 years ago by julianneradford ▴ 20
1
vote
3
replies
2.1k
views
Prokka only creates .log file
miniconda prokka ubuntu bioconda
4.6 years ago by Camila Martínez ▴ 40
0
votes
0
replies
1.6k
views
News: Bioinformatics Open Source Conference 2021
OBF BOSC Conference
4.6 years ago by Chris Fields ★ 2.2k
4
votes
3
replies
3.9k
views
Hierarchical Clustering of GO terms
Clustering GO similarity Ontology
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 180
122,202 results • Page 681 of 2445
Recent Votes
Comment: low quality data or file name swapping -- cellranger arc errors when processing
Comment: low quality data or file name swapping -- cellranger arc errors when processing
A: Regarding Microarray Platforms
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
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Recent Replies
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
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…
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