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122,202 results • Page 669 of 2445
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4
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2
replies
1.5k
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Need help in doing proteomics analysis
proteomics
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 30
0
votes
0
replies
967
views
Job: Postdoctoral Researcher in Computational Biology
computationalbiology germany microbiome postdoc
4.6 years ago by melanie.schirmer ▴ 10
0
votes
2
replies
834
views
Design an algorithm for identifying long AT runs of more than 5 times.
DNA
4.6 years ago by Siva • 0
0
votes
0
replies
1.0k
views
Metaquast largest contig by species identical for most species in the metagenomic assembly
metagenomics species quast contig metaquast
4.6 years ago by Matteo Schiavinato ★ 3.7k
2
votes
4
replies
2.8k
views
CPM threshold for RNASeq count data
Count RNASeq cpm filtering edgeR
4.6 years ago by Will ▴ 20
0
votes
0
replies
373
views
How to convert the to ratio
sum-of-pairs
4.5 years ago by aa • 0
0
votes
0
replies
716
views
plink - generate VCF
plink
4.6 years ago by esimonova.me ▴ 30
0
votes
1
reply
869
views
Given a disease name, which R package can return relevant tissues of pathogenic?
pathogenic tissue-of-disease
4.6 years ago by Shicheng Guo ★ 9.6k
0
votes
1
reply
1.1k
views
Reactome physical association pairs in the human protein-protein interactions data
reactome network ppi
updated 4.6 years ago by 27k • written 4.6 years ago by ▴ 100
2
votes
3
replies
2.2k
views
Can I combine both single and paired end RNA-seq replicates for analysis?
RNA-seq sequencing
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
3
votes
6
replies
3.2k
views
Samtools view does not output all reads
samtools bam
4.6 years ago by b10hazard • 0
0
votes
2
replies
1.3k
views
How to achieve the goal "only genes with non-zero expression values in at least half of the sample type were kept"
RNA-seq TCGA
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
0
votes
2
replies
1.7k
views
How to filter up and down regulated genes in a list of DE genes from DEseq?
upanddownregulated genes
updated 4.6 years ago by ▴ 60 • written 4.6 years ago by • 0
0
votes
0
replies
658
views
TargetScan query with "3prime pairing", "context+ score" with R
R targetscan
4.6 years ago by ahadli.farid ▴ 50
0
votes
0
replies
749
views
Coverage vs Identity, which is more important ?
blast genes
4.6 years ago by ddh8602 • 0
1
vote
2
replies
1.1k
views
Modifying dataframe in R based on Unique values in 2nd column
R dataframe
4.6 years ago by salman_96 ▴ 70
0
votes
3
replies
1.1k
views
Rna seq analysis
factors transcription motif
4.6 years ago by rheab1230 ▴ 150
5
votes
6
replies
2.3k
views
How to structure my edgeR model to incorporate a temporal variable and 2 categorical variables?
edgeR differential-gene-expression glm r
4.6 years ago by O.rka ▴ 750
0
votes
0
replies
822
views
Watterson Estimate VCFs with different coverage
software vcf popgen
4.6 years ago by timothy.delory ▴ 20
4
votes
3
replies
2.5k
views
Scatterplot ggplot: too many overlapping point make an area magnified/ increase specific areas
overlapping ggplot scatterplot r
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 160
1
vote
3
replies
1.2k
views
found unannotated gene via rna-seq, can i use public datasets (raw data) to find clinical info about this gene?
rna-seq lncrna
updated 4.6 years ago by 45k • written 4.6 years ago by • 0
0
votes
2
replies
1.3k
views
design matrix considering treatment, timepoints and batches
limma design microarray experimental
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 60
1
vote
3
replies
1.3k
views
Sequencing coverage for phylogenomic studies
philogenomics Nestseq Rnaseq
4.6 years ago by tiagobellintani ▴ 40
0
votes
1
reply
983
views
How to compare enrichment scores?
enrichment scores
updated 4.6 years ago by ★ 90k • written 4.6 years ago by • 0
1
vote
3
replies
1.6k
views
Gene annotation BLAST results only finding one hit
BLAST Gene-Annotation Pathwaysproject D.takahashii
updated 4.6 years ago by 16k • written 4.6 years ago by • 0
1
vote
1
reply
4.2k
views
Filter SingleCellExperiment object just by one gene expression
SingleCellExperiment
updated 4.6 years ago by 4.2k • written 4.6 years ago by ▴ 590
1
vote
5
replies
1.7k
views
R and GEO
GEO
updated 4.4 years ago by 45k • written 4.6 years ago by • 0
0
votes
4
replies
1.7k
views
How to select algorithm model for PRS score predict disease?
PRS Prediction Model
4.6 years ago by li • 0
4
votes
4
replies
1.7k
views
Project for a beginner
python Project beginners
updated 4.4 years ago by 45k • written 4.6 years ago by • 0
0
votes
3
replies
1.6k
views
Jointly calling samples from different studies, which have different read lengths?
joint variant gatk calling
updated 4.6 years ago by ▴ 110 • written 4.6 years ago by ▴ 60
0
votes
2
replies
992
views
RNAseq Per tile sequence quality question
RNAseq fastqc
4.6 years ago by cook.675 ▴ 250
0
votes
1
reply
1.1k
views
Question about ExomeDepth's output
software error R
updated 4.6 years ago by 154k • written 4.8 years ago by • 0
5
votes
0
replies
1.6k
views
News: Bioinformatics Contest 2021
bioinfcontest contest bioinforussia
updated 2.8 years ago by 45k • written 4.6 years ago by ▴ 50
1
vote
4
replies
3.9k
views
Using ExomeDepth for GRCH38 processed samples to call CNVs
Exome GrCh38 ExomeDepth CNV
updated 2.2 years ago by ▴ 220 • written 4.8 years ago by ▴ 40
9
votes
19
replies
6.2k
views
duplicate gene IDs with different length after cd-hit-est dereplicate and cluster
replicate duplicate cd-hit cluster
4.6 years ago by phxu6780 • 0
0
votes
0
replies
1.3k
views
Job: Bioinformatician @IGC - Portugal
bioinformatician facility
4.6 years ago by antonioggsousa 3.4k
0
votes
1
reply
777
views
Database Containing Hla Alleles And Snps
allele HLA
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
3
votes
3
replies
3.9k
views
New to ATAC-seq single cell
atac-seq peak
updated 4.6 years ago by 9.0k • written 4.6 years ago by ★ 4.4k
3
votes
3
replies
2.7k
views
Negative heritability and filtering summary statistics
ldsc partitioned heritability
3.2 years ago by gokberk ▴ 90
0
votes
1
reply
892
views
GenomeStudio in a cloud service
genomestudio aws
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
1
vote
1
reply
1.3k
views
Correcting for batch effect in survival data
survival batch-effect
updated 15 months ago by 45k • written 4.6 years ago by ▴ 300
2
votes
5
replies
8.7k
views
Error in loadNamespace(name) : there is no package called ‘shiny’
MetaQc R R-studio Geodatasets MetaOmics
4.6 years ago by xxxxxxxx ▴ 20
8
votes
3
replies
2.0k
views
Getting libType without running quantification with Salmon
strandness salmon rnaseq python strand
updated 4.6 years ago by 7.2k • written 4.6 years ago by ▴ 140
0
votes
2
replies
916
views
Genome search on FTP NCBI
NCBI
4.6 years ago by Debut ▴ 20
7
votes
12
replies
2.8k
views
Failing to run tblastn
tblstn blast
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 70
0
votes
0
replies
684
views
Snakemake only reads the target rule and not the other rules
Snakemake
4.6 years ago by rudylu.monica • 0
0
votes
2
replies
1.2k
views
How to do damage calibration after vg map
vgtool vg PMD aDNA
4.6 years ago by puddingmeow516 ▴ 10
0
votes
0
replies
892
views
Why ABSOLUTE calculate CCF=NA?
ABSOLUTE
4.6 years ago by Laven9 • 0
1
vote
1
reply
1.2k
views
Detecting Human Contamination in Low Coverage NGS sample
verifybamid CalculateContamination
4.6 years ago by igorm ▴ 20
2
votes
3
replies
1.5k
views
Is there a way to include not conda package/programs to snakemake environment?
Non-Conda_packages Snakemake
4.6 years ago by lmlukoseviciute ▴ 60
122,202 results • Page 669 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?
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Recent Replies
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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