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122,202 results • Page 670 of 2445
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transition plot between chromatin states from non-tumour to tumour sample
Gmisc R
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 30
0
votes
0
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863
views
remove from mummerplot some contigs
mummerplot mummer
4.6 years ago by shinken123 ▴ 150
0
votes
0
replies
799
views
using TREEMM for identification of bipartite motifs in promoter sequences
CLUSTERS TREEMM PROMOTER
4.6 years ago by madhujamano • 0
6
votes
8
replies
2.4k
views
Diseases related pathways
pathways wikipathway kegg reactome
updated 4.6 years ago by ▴ 590 • written 4.9 years ago by ▴ 80
1
vote
2
replies
2.3k
views
Understanding why `Design matrix not of full rank. The following coefficients not estimable` during GLM
edgeR design-matrix differential glm offtopic
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 750
0
votes
0
replies
864
views
PAML (CODEML) with 0 branch lengths
PAML codeml
4.6 years ago by DNAlias ▴ 40
1
vote
8
replies
2.5k
views
DESeq2 comparison two cell types and two genotypes
DESEQ2
updated 4.6 years ago by ★ 1.9k • written 4.6 years ago by • 0
0
votes
0
replies
584
views
Extracting Position-specific di-amino acid propensity(PSTAAP) features
protein features propensity sequences
4.6 years ago by suresh.wrc • 0
1
vote
0
replies
657
views
The best way to find cell differentiation path
differentiation fate biology fibroblasts scRNA-seq
4.6 years ago by fifty_fifty ▴ 90
3
votes
2
replies
1.4k
views
Plink/VCFTools pairwise LD is always 1
disequilibrium LD plink linkage vcftools
4.6 years ago by pmc.sa ▴ 40
0
votes
1
reply
879
views
modify name field from genbank file
gb genebank gene GATU
updated 4.6 years ago by ★ 30k • written 4.6 years ago by • 0
0
votes
5
replies
2.1k
views
Consensus deduplication issues with non-matching/'slippy' primers?
DNA-seq deduplication
updated 4.6 years ago by 22k • written 4.6 years ago by ▴ 110
0
votes
0
replies
531
views
RNA sequencing analysis pipeline for micro RNA mutants
sequencing RNA
4.6 years ago by aranyak111 • 0
4
votes
5
replies
2.8k
views
how to understand the P value of the Deseq2 results
statistics p_value DEseq2
updated 4.6 years ago by ★ 2.6k • written 4.6 years ago by ▴ 130
0
votes
1
reply
978
views
Retrieving One-to-One Orthologs of Unprocessed cDNAs
sequencing orthologs
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
5
votes
2
replies
2.3k
views
Is it technically correct to eliminate branches with low bootstrap ?
phylogenetics
updated 4.6 years ago by ★ 30k • written 4.6 years ago by • 0
1
vote
1
reply
1.3k
views
Remove duplicate SNPs by allele frequency in PLINK
QC plink
updated 4.6 years ago by 11k • written 4.6 years ago by • 0
0
votes
3
replies
1.1k
views
Possibility of using 10x Genomics reads from another individual
genome-assembly
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
3
replies
2.1k
views
Abnormal GC content in Whole Exome Sequencing Sample after alignment
library WES GC Sequencing FASTQC
updated 4.1 years ago by • 0 • written 4.6 years ago by • 0
0
votes
2
replies
1.5k
views
Find the publication of the dataset available in NCBI's SRA Library
SRA 16s NCBI
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 50
6
votes
12
replies
4.3k
views
BAI index format
BAI index BAM CSI
4.6 years ago by maxrwjones ▴ 60
4
votes
10
replies
7.5k
views
7 follow
Unable to find adapter seq using Fastp
sequencing sequence assembly software error fastp
updated 4.6 years ago by ★ 2.9k • written 7.1 years ago by • 0
4
votes
7
replies
2.5k
views
Variable numbers of Reads. I'm lost
Nanopore featureCount Alignment Sequencing Reads
updated 4.6 years ago by 48k • written 4.6 years ago by • 0
2
votes
3
replies
2.4k
views
Using VEP custom on ClinVar error - Couldn't find index.
vep custom ensembl clinvar
4.6 years ago by milwaukee • 0
2
votes
2
replies
3.5k
views
get count matrix from bam files
bam ATAC-seq
updated 2.5 years ago by 45k • written 4.6 years ago by ▴ 70
0
votes
1
reply
835
views
Array express microarray single channel agilent data only contain Green.DerivedSignal values??
microarray r
updated 4.6 years ago by ★ 90k • written 4.6 years ago by ▴ 30
4
votes
1
reply
1.3k
views
How to trim alignments in a BAM file to a restricted genomic window?
bam alignment
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 90
6
votes
5
replies
1.8k
views
6 follow
Remove 2nd colon and rest of the values in a dataframe using R/ Unix
coordinates SNP Unix R
updated 4.6 years ago by 12k • written 4.6 years ago by ▴ 70
3
votes
4
replies
2.9k
views
FeatureCounts total alignment = 0. Can you help me please
Nanopore RNAseq Bam featureCounts NGS
updated 4.6 years ago by 103k • written 4.6 years ago by • 0
4
votes
5
replies
2.2k
views
De novo assembly of chloroplast genome
Scaffolding Illumina assembly
updated 4.6 years ago by ★ 1.8k • written 4.6 years ago by ▴ 20
0
votes
2
replies
2.2k
views
FastQC per sequence GC content
FastQC GCcontent qualitycontrol
4.6 years ago by jhy ▴ 10
1
vote
2
replies
1.2k
views
Ensembl fasta DNA data
ensembl genome mitochondria
4.6 years ago by kb_93 ▴ 10
2
votes
1
reply
848
views
Reconstructing an incomplete transcript of interest
RNAseq transcriptomics NGS
updated 4.6 years ago by ★ 1.8k • written 4.6 years ago by ▴ 30
0
votes
24
replies
5.3k
views
converting spaces to tabs in gtf files
NCBI
4.6 years ago by storm1907 ▴ 30
0
votes
0
replies
637
views
correlation of WGBS dataset and RNAseq dataset
transcription methylation
4.6 years ago by frylhc • 0
0
votes
1
reply
1.0k
views
Using nhmmer to identify gene members of a superfamily
genes nhmmer profilehmmer hmmer
updated 3.8 years ago by • 0 • written 4.6 years ago by ▴ 60
0
votes
4
replies
1.4k
views
Add all non overlapping genes/transcripts from one gtf to another with bedtools intersect
bedtools annotation gtf
4.6 years ago by robert.murphy ▴ 110
10
votes
8
replies
5.3k
views
Can Plink Be Used For The Analysis Of A Bacterial Dataset?
plink
updated 4.6 years ago by ▴ 10 • written 12.5 years ago by ▴ 40
0
votes
1
reply
2.4k
views
What is the best way to perform a PCA on .vcf of closely related bacteria?
variant-calling
updated 20 months ago by 45k • written 4.6 years ago by ▴ 10
2
votes
2
replies
2.1k
views
How to get chromosomal position of list of RS number(GRCh38)?
Genome SNP GRCh38 Polymorphism
4.4 years ago by Yoosef ▴ 60
3
votes
6
replies
2.3k
views
BLAST Database error: No alias or index file found for protein database
blast
updated 4.6 years ago by 16k • written 4.6 years ago by • 0
0
votes
0
replies
725
views
comparing distinct peaks from riboseq profiling results
ribosomal-profiling ribo-seq peaks
4.6 years ago by Assa Yeroslaviz ★ 1.9k
4
votes
3
replies
2.9k
views
Liftover vs Ensembl Crossmap
crossmap liftover converter assembly ensembl
4.6 years ago by Thind amarinder ▴ 340
1
vote
1
reply
815
views
tped files to bed with awk
plink
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 30
10
votes
32
replies
6.0k
views
6 follow
Why my CD31+ endothelial cells RNAseq didn't express CD31?
CD31 HISAT2 endothelialcells Stringtie RNAseq
4.6 years ago by Youyy • 0
290
votes
55
replies
20k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 2.8 years ago by 45k • written 12.6 years ago by 10k
0
votes
2
replies
1.3k
views
How to add GO annotation terms (molecular function, component, biological process) to my results (DESeq2 RNA-seq analysis) in RStudio?
annotation rnaseq deseq2 goterms rstudio
updated 4.6 years ago by ▴ 220 • written 4.6 years ago by • 0
0
votes
1
reply
1.3k
views
GFF/GTF file download from UCSC or gnomAD
GFF
updated 4.6 years ago by 9.3k • written 4.6 years ago by ▴ 30
0
votes
4
replies
2.2k
views
Low GQX
GQX
4.6 years ago by sisalem • 0
1
vote
2
replies
1.1k
views
MicroArray MetaAnalyse: Help Criticise/Suggest Better Idea for PhD thesis
Microarray GWAS Network Metaanalysis
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 60
122,202 results • Page 670 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 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…
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 …
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