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122,200 results • Page 613 of 2444
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3
votes
36
replies
8.0k
views
inquiry related to snpsift
rsid snp vcf
updated 4.3 years ago by ★ 90k • written 4.3 years ago by ▴ 150
2
votes
3
replies
1.3k
views
Kallisto quantification
kallisto RNA-Seq
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
0
votes
0
replies
2.6k
views
How to control the order of cells in dittoHeatmap for scRNAseq data analysis?
Cell scRNA dittoHeatmap Single
4.3 years ago by FantasticAI ▴ 60
0
votes
5
replies
2.0k
views
Multivariable Design in EdgeR (Design matrix / model.matrix) - Tilde Use
edgeR R
4.3 years ago by Noah E. ▴ 20
14
votes
7
replies
5.9k
views
Difference between a bin and a MAG
metagenomics mags binning
updated 3.9 years ago by ▴ 140 • written 4.3 years ago by ▴ 30
9
votes
5
replies
4.1k
views
Analysis of shRNA/CRISPR screens in 2021
crispr shrna
updated 4.2 years ago by ★ 7.8k • written 4.3 years ago by 90k
9
votes
9
replies
2.9k
views
Forum: Opinions on publishing Research as a Blog?
bioinformatics publishing
4.3 years ago by ponganta ▴ 590
1
vote
3
replies
2.3k
views
Running Salmon RNA quantification with pre-computed index
salmon RNAseq
4.3 years ago by saipra003 ▴ 20
0
votes
1
reply
1.0k
views
Retrieve reads overlapping indels
variants reads indel
updated 4.3 years ago by 9.8k • written 4.3 years ago by ▴ 290
0
votes
0
replies
717
views
Criteria to be used to select top 10 hub genes for salt tolerance in rice using cytohubba
analysis cytohubba hubgenes criteria
updated 4.3 years ago by 154k • written 4.3 years ago by • 0
15
votes
8
replies
4.7k
views
8 follow
Would this laptop be sufficient for small dataset/sequence analysis?
DeSEQ2 tcga Xena laptop
4.3 years ago by BioinformaticsEnthusiast • 0
15
votes
6
replies
12k
views
Matplotlib comprehensive chromosome drawing
matplotlib python
updated 2.9 years ago by 45k • written 10.4 years ago by ▴ 530
3
votes
3
replies
3.2k
views
When to merge sequencing data from multiple lanes (FastQToSam, SamToFastq, BWA, MergeBamFiles, or additional step)?
alignment pipeline ngs picard sequencing
updated 4.3 years ago by 16k • written 4.3 years ago by ▴ 60
0
votes
2
replies
1.9k
views
fineRADstructure file error
finestructure fineradstucture structure SNP RADseq
updated 4.3 years ago by • 0 • written 6.1 years ago by ▴ 60
2
votes
3
replies
2.7k
views
How to fill taxonomy informations from NCBI?
Taxonomy NCBI
updated 4.3 years ago by 8.7k • written 4.3 years ago by • 0
11
votes
9
replies
12k
views
How to generate a .sam/.bam file of a particular chromosome or even a particular region?
alignment genome next-gen
updated 3.8 years ago by 45k • written 11.0 years ago by ▴ 260
0
votes
1
reply
845
views
Calculate mean number of loci per taxon
phylogenetic multi-locus statistics loci
updated 4.3 years ago by ★ 1.7k • written 4.3 years ago by ▴ 10
0
votes
0
replies
727
views
Virus-Host Interactions [Any help/suggestion appreciated]
Interaction Ligand Receptor Virus-Host
4.3 years ago by eoz222 • 0
2
votes
1
reply
1.6k
views
Forum: Job opportunities in Europe, with and without a PhD
PhD career
updated 5 months ago by ★ 90k • written 4.3 years ago by ▴ 40
0
votes
1
reply
983
views
conserved region in html file
MSA html conserved region
updated 4.3 years ago by ★ 1.7k • written 4.3 years ago by • 0
104
votes
34
replies
130k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 22 months ago by 45k • written 13.5 years ago by ▴ 390
1
vote
4
replies
5.2k
views
Removing genes of Seurat object during integration pipeline
genes filtering remove seurat integration
4.3 years ago by Stevens ▴ 30
0
votes
3
replies
2.2k
views
error related to SnpSift
rsid SnpSift SNP
updated 2.1 years ago by • 0 • written 4.3 years ago by ▴ 150
0
votes
4
replies
1.8k
views
Minfi - estimateCellCounts
CellCounts minfi
4.3 years ago by abnerapsley • 0
13
votes
12
replies
5.1k
views
Displaying points which fall outside of the plot window in EnhancedVolcano
EnhancedVolcano plot volcano
4.3 years ago by os306 ▴ 10
0
votes
1
reply
895
views
Error: RSEM Bam file for variant calling
Transcriptome Variant BCFTOOLS RSEM calling
4.3 years ago by kartikayprasad ▴ 10
1
vote
1
reply
1.3k
views
Network construction and analysis using WGCNA
meta-analysis WGCNA
updated 4.3 years ago by 3.9k • written 4.3 years ago by ★ 1.9k
0
votes
0
replies
705
views
How to add enzyme details in Tassel pipeline?
GBS Tassel GBSEnzyme.java
updated 4.3 years ago by 5.9k • written 4.3 years ago by ▴ 80
34
votes
26
replies
22k
views
13 follow
Reliable Fastq compression programs
fastq compression reliability
updated 3.0 years ago by ▴ 330 • written 10.1 years ago by 11k
0
votes
0
replies
738
views
Phylip file
iqtree alignment Vcf vcf2phylip
4.3 years ago by Kagisoralph • 0
2
votes
2
replies
1.5k
views
How to a determine and output if numbers in matrix are above a certain value?
Unix depth matrix coverage line command
4.3 years ago by YL ▴ 10
0
votes
0
replies
692
views
Interspecific read alignment - Eukaryote
illumina align genome reads organism
4.3 years ago by maxime.policarpo ▴ 200
2
votes
7
replies
3.4k
views
down regulated and up regulated using r
RNA-Seq
updated 3.4 years ago by 45k • written 4.4 years ago by ▴ 10
0
votes
0
replies
703
views
MSA of single copy gene sequences using OrthoVenn2 output
phylogenetic alignment tree msa orthovenn
4.3 years ago by shanewidanagama • 0
0
votes
0
replies
828
views
Job: Postdoctoral Researcher in Bioinformatics and Genetics - Washington, D.C
Postdoc
4.3 years ago by shaolei.teng • 0
0
votes
3
replies
2.6k
views
Is there any tool that can convert gene bank format (.gbff) file to gff3 format ?
genbank gff
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
1
vote
0
replies
830
views
Adjusting batch effects for this specific study design using ComBat
Batch-effect ComBat
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 10
0
votes
0
replies
969
views
Job: Bioinformatics Scientist/ Scientific Data Curator
biologist dbGap
updated 2.7 years ago by 45k • written 4.3 years ago by ▴ 90
0
votes
0
replies
946
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
RNA-seq Transcriptomics
updated 2.5 years ago by 45k • written 4.3 years ago by ▴ 20
0
votes
1
reply
1.7k
views
WES Agilent SureSelect Human All Exon V7
Agilent WES Pipeline SureSelect
updated 4.3 years ago by ▴ 840 • written 4.3 years ago by • 0
1
vote
4
replies
1.9k
views
extracting Genus abundance info from Kraken 2 output file
kraken2
updated 4.3 years ago by ★ 1.7k • written 4.3 years ago by ▴ 110
3
votes
4
replies
3.4k
views
Removal of host reads from shotgun metagenomics data.
metagenomics shotgun
updated 4.3 years ago by 154k • written 4.3 years ago by • 0
2
votes
2
replies
1.2k
views
Different coverage depth
alignment
4.3 years ago by wes ▴ 90
0
votes
6
replies
3.2k
views
how can i convert my gene list to a format that reactome recognises?
gene pathway-analysis reactome
updated 4.3 years ago by 45k • written 9.5 years ago by ▴ 280
0
votes
2
replies
1.8k
views
Output from macs subcommand 'bdgpeakcall'
Output macs header
4.3 years ago by arsala521 ▴ 60
0
votes
2
replies
1.1k
views
Rows of read count files
RNA-seq
4.3 years ago by Abhishek • 0
0
votes
0
replies
1.1k
views
Problems with QIAseq spike-in normalization
QIAseq RNA-seq DEA normalization
4.3 years ago by lluc.cabus ▴ 30
3
votes
4
replies
2.8k
views
color coded PCA plot in R for a combined set
plink pca plot
4.3 years ago by raalsuwaidi ▴ 110
8
votes
8
replies
4.2k
views
Render Rmarkdown in nextflow
rmarkdown nextflow
updated 4.3 years ago by 9.3k • written 4.5 years ago by 90k
2
votes
1
reply
677
views
FastQC is not recognising that there are adaptors
fastqc
updated 4.3 years ago by ★ 19k • written 4.3 years ago by • 0
122,200 results • Page 613 of 2444
Recent Votes
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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Recent Replies
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…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
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