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News: Online Training - Conservation Genomics
Genome Genomics ConservationGenomics SNPs
4.5 years ago by Physalia-courses ★ 2.7k
2
votes
1
reply
1.7k
views
Convert GFF3 to splice junction BED file, for filtering variants multi-sample (RNA-seq) VCF
rna splice-junction vcf
4.6 years ago by William ★ 5.4k
0
votes
3
replies
1.6k
views
How to find single copy family from InParanoid output
InParanoid single copy
updated 4.6 years ago by ★ 2.9k • written 4.6 years ago by ▴ 20
0
votes
0
replies
1.7k
views
No peaks found in Signac's FindMarker
seurat atac-seq Signac atac singlecell
4.6 years ago by ahmad mousavi ▴ 800
6
votes
4
replies
1.7k
views
Concatenating fasta files based on prefix ?
aligment RNA DNA fasta
updated 4.6 years ago by 11k • written 4.6 years ago by ▴ 1000
15
votes
10
replies
4.7k
views
How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
transcript rna-seq
updated 4.6 years ago by ▴ 100 • written 4.6 years ago by • 0
0
votes
2
replies
1.1k
views
Database/list of disease complications
complications database disease
updated 4.6 years ago by ▴ 20 • written 4.6 years ago by • 0
0
votes
2
replies
1.8k
views
Is it possible to annotate a file for the human genome using the command line without using an amino acid sequence
Annotation human DNA PROVEAN
4.6 years ago by kamanovae ▴ 100
1
vote
0
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1.1k
views
braker2 output: gff file is missing and species folder is empty
prothint braker2 genome braker annotation
updated 4.6 years ago by 12k • written 4.6 years ago by ▴ 40
0
votes
2
replies
1.3k
views
Does GISAID fasta files contain spike protein or whole genome sequence?
sequence protein spike genome
updated 4.6 years ago by 48k • written 4.6 years ago by • 0
2
votes
0
replies
1.1k
views
Job: ELIXIR Training Coordinator (pan-European bioinformatics training)
training lifescience
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 470
1
vote
4
replies
2.1k
views
Why GC content is important on NIPT results?
NGS NIPT Sequencing
4.6 years ago by khanhlpbao • 0
1
vote
4
replies
2.4k
views
Variant calling from comparison of assembled genomes where there is only one read depth.
variant
updated 4.6 years ago by ▴ 640 • written 4.6 years ago by ▴ 150
3
votes
2
replies
1.6k
views
Finding all instances of a recurring motif in a repeat protein
repeat markov alignment motifs
4.6 years ago by NeuralCode ▴ 10
0
votes
0
replies
583
views
rpy hgu133a.db loading error
hgu133a.db python rpy
4.6 years ago by dxodnd • 0
4
votes
4
replies
4.2k
views
Help with CNV calling using ExomeDepth
exomedepth R CNV gCNV exome
updated 4.6 years ago by ▴ 50 • written 5.0 years ago by ▴ 130
2
votes
1
reply
1.2k
views
How to grep scaffold from the vcf file
introns VCF scaffolds
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 170
0
votes
1
reply
1.1k
views
For loop - mkdir and command
bash
updated 2.4 years ago by 45k • written 4.6 years ago by • 0
2
votes
6
replies
4.2k
views
why my volcano plot looks strange?
wilcox.test RNAseq Metabolomics LCMS
updated 4.6 years ago by 21k • written 4.6 years ago by ▴ 40
0
votes
3
replies
6.9k
views
How to interpret multiqc report
QC multiqc rna-seq
updated 4.6 years ago by ★ 1.5k • written 4.6 years ago by ▴ 30
5
votes
2
replies
2.3k
views
Can you suggest any journal without any publication fee for publishing microbiology and bioinformatics papers?
journals microbiology publications
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 20
3
votes
1
reply
1.4k
views
How to get all microRNA target genes?
miRNA multimir microRNA targetgenes tarbase
updated 4.6 years ago by 22k • written 4.6 years ago by ▴ 10
1
vote
3
replies
3.6k
views
vcftools intersect vs bedtools intersect
bedtools vcf vcftools
updated 4.3 years ago by 45k • written 4.6 years ago by • 0
2
votes
4
replies
4.7k
views
How to extract sequences from fasta that have a certain length ?
minlength fasta
updated 4.6 years ago by 8.7k • written 4.6 years ago by ▴ 140
2
votes
5
replies
1.5k
views
Plotting Differential Induced Genes across timepoints in DESEQ2
Bioconductor MA RNA-seq DESEQ2
4.6 years ago by raisamathenge ▴ 30
0
votes
5
replies
5.5k
views
How to highlight DE genes in plotMD ?
edgeR plotMD volcanoplot mirnaseq
updated 4.6 years ago by • 0 • written 7.6 years ago by ▴ 110
15
votes
7
replies
2.5k
views
6 follow
Forum: What to put in my Github
Github
updated 4.6 years ago by ★ 3.3k • written 4.6 years ago by ▴ 20
0
votes
0
replies
697
views
What criteria follow in order to choose the crystaline structure of a molecule
Molecular Docking
4.6 years ago by roybatty269 • 0
2
votes
2
replies
1.7k
views
Recombination maps for cattle
SNP IMPUTE2 genome Assembly
updated 4.6 years ago by • 0 • written 6.2 years ago by ▴ 10
2
votes
2
replies
1.6k
views
Samtools view filter by reference sequence
samtools
4.6 years ago by maxrwjones ▴ 60
0
votes
0
replies
709
views
The effect of heterozygosity on genome alignment
heterozigosity alignment bwa sequence
4.6 years ago by Iseez • 0
0
votes
2
replies
2.4k
views
Segmentation fault (core dumped) error in MUSCLE
NGS alignment fastq linux sequence
4.6 years ago by steel1990 ▴ 20
0
votes
1
reply
710
views
Genome sequencing data analysis and assembly L.lactis subsp.lactis strain Lac3
well
updated 4.6 years ago by ★ 30k • written 4.6 years ago by • 0
4
votes
1
reply
1.1k
views
Is it bad practice to change threshold for interaction probability?
STRING Cytoscape
updated 4.6 years ago by 9.0k • written 4.6 years ago by ▴ 20
7
votes
8
replies
3.3k
views
bedops wig2bed 'Row begins with a tab or space' error
wig2bed bedops convert2bed
updated 4.6 years ago by 36k • written 4.6 years ago by ▴ 40
0
votes
2
replies
1.1k
views
correlation analysis of a single variable versus multiple variables
correlation r RNA-Seq
4.6 years ago by pinheirofabiano ▴ 130
1
vote
0
replies
685
views
Holistic enzyme activity determination with computation
proteomics protein enzymes
updated 4.4 years ago by 45k • written 4.6 years ago by ▴ 10
0
votes
5
replies
1.5k
views
transcription factor activation order
transcription
updated 4.6 years ago by 90k • written 4.6 years ago by • 0
0
votes
0
replies
580
views
JoinMap4 makes a new map every time
joinmap linkage_mapping genetic_map SNP
4.6 years ago by Beetle Editor • 0
0
votes
3
replies
3.5k
views
LDSC -Genetic correlation, some results all have NA valuies
correlation ldsc genetic gwas
updated 4.6 years ago by ★ 4.8k • written 4.6 years ago by • 0
0
votes
4
replies
2.3k
views
Can Meta-GWAS summary statistic results be used for Meta-GWAS (For example, METAL)?
METAL input Meta-analysis Meta-GWAS
4.6 years ago by li • 0
4
votes
6
replies
2.1k
views
Batch effect correction of 2 studies with different covariates
batch-effect R RNA-seq
updated 4.6 years ago by ★ 2.9k • written 4.6 years ago by ▴ 20
1
vote
2
replies
1.7k
views
MemoryError w/ matrix | Smith-Waterman Algorithm Python
Python Smith-Waterman
updated 20 months ago by 45k • written 4.6 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Job: Informatician / Data Analyst | University of Glasgow
data-analyst
updated 2.5 years ago by 45k • written 4.6 years ago by 15k
1
vote
3
replies
2.2k
views
IndexError: list assignment index out of range | Needleman-Wunsch Algorithm - Python
Python Needleman-Wunsch Dynamic-Programming
updated 20 months ago by 45k • written 4.6 years ago by ▴ 10
1
vote
2
replies
1.9k
views
Pooling normal data in Mutect2
mutect2 pooling normal samples panelofnormals
4.6 years ago by Michelle • 0
17
votes
4
replies
6.2k
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin samtools bcftools vcf split-vep
updated 3.2 years ago by ▴ 250 • written 4.6 years ago by ★ 4.5k
0
votes
0
replies
1.1k
views
integration of single cell RNA-seq and bulk RNA-seq data
RNA-seq
4.6 years ago by ramyak1912 • 0
3
votes
4
replies
2.1k
views
how to extract REF and ALT DNA string around SNV
SNV motif
4.6 years ago by shangguandong1996 ▴ 30
0
votes
0
replies
625
views
Minimum enrichment score to take for analysis
Sequencing Rna-Seq
4.6 years ago by ashwing.kofficial ▴ 10
122,202 results • Page 680 of 2445
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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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