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93 results • Page 2 of 2
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0
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0
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128
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Mitogenomes gap closure and making circular genome
gapclosure Mitogenomes validation circulargenome
4 days ago by KHURRAM SHAHZAD • 0
1
vote
0
replies
125
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Help with VG Toolkit: VCF Output is Empty
vg
updated 4 days ago by 161k • written 4 days ago by ▴ 10
1
vote
1
reply
125
views
Conda severely broken after attempting mamba install
biopython conda mamba pycosat
updated 1 day ago by 3.6k • written 1 day ago by ▴ 30
0
votes
5
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122
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
55 minutes ago by SilhouetteQ • 0
0
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0
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121
views
Clarification on StringTie's `--merge` parameters
stringtie stringtie-merge
5 days ago by DGTool • 0
0
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0
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118
views
How to implement an IGV to streamlit app?
python streamlit igv
4 days ago by avigail.shnaider • 0
0
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0
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117
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria Metagenomics Database
5 days ago by Christopher • 0
0
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0
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115
views
Error while loading model of Spatial data deconvolution using cell2location
Python cell2location
updated 4 days ago by 43k • written 4 days ago by ▴ 50
0
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0
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113
views
Xenium multi sample data
batch annotation cell Xenium effect
2 days ago by Omics data mining ▴ 260
0
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0
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112
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep vcf gnomad
1 day ago by asalimih ▴ 60
0
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0
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110
views
Cox Model with interaction item interpretation
Cox
4 days ago by Bine ▴ 60
0
votes
0
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108
views
Get Paired TCRa/b from MIXCR
python r mixcr tcr_seq
3 days ago by Scott McKay ▴ 30
0
votes
0
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107
views
Imputation of missing genotypes
panel beagle imputation
3 days ago by analyst ▴ 50
0
votes
0
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105
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair samtools alignment
1 day ago by Zeng Hao ▴ 40
0
votes
0
replies
104
views
vdjtools
vdjtools
4 days ago by yueli7 ▴ 250
0
votes
0
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104
views
Cellphonedb results
cpdb visulization cellphonedb
3 days ago by piotto ▴ 20
0
votes
1
reply
103
views
When should I use R-MarkDown over R-Script ?
r rscript rmarkdown
updated 8 hours ago by 82k • written 12 hours ago by ▴ 160
1
vote
0
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102
views
What is Deepvariant default filtering values ?
vcf calling filter variant deepvariant
1 day ago by Shae ▴ 10
0
votes
1
reply
101
views
input file for alternative splicing in rmats in linux
rmats
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
2
replies
101
views
LncRNA Nomenclature
ENST nomenclature lncrna GBB ENSG
10 hours ago by jain72744 ▴ 10
0
votes
0
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100
views
Summary Statistics SNPs not found in Target data
SNP plink PRS
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
0
replies
100
views
how to downlad slices of CRAM fro ICGC ARGO
icgc samtools cram
1 day ago by Javier • 0
0
votes
0
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100
views
Normalizing AMR gene count data
abundance RGI
updated 4 days ago by 43k • written 4 days ago by ▴ 100
0
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0
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99
views
meffil.snp.concordance
meffil methylation snp_concordance
2 days ago by kyj222637 • 0
0
votes
0
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96
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS WGS Pathway denovo
updated 1 day ago by 43k • written 1 day ago by ▴ 90
0
votes
0
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93
views
monocle 3-- Could not get node in small cluster
monocle3
2 days ago by synat.keam ▴ 100
3
votes
1
reply
86
views
Question about methylation location
Methylation WGBS bisulfide
updated 5 hours ago by ★ 1.9k • written 17 hours ago by • 0
0
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0
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85
views
Generating .bed file and .map file for polyploid vcf file through plink
bed polyploid map plink
2 days ago by analyst ▴ 50
0
votes
1
reply
81
views
Microbial Signal Transduction Database
MiST
updated 8 hours ago by 11k • written 10 hours ago by • 0
0
votes
0
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73
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo WGS DNA-seq assembling
1 day ago by Matvii Mykhailichenko • 0
0
votes
3
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68
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk vcf converter liftover
updated 2 hours ago by ▴ 390 • written 3 hours ago by ▴ 260
0
votes
0
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68
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization Mendelian two-sample
21 hours ago by Nikki • 0
0
votes
0
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67
views
How do I calculate SE or P value if I only have BETA
prscsx beta se pvalue
updated 8 hours ago by 11k • written 19 hours ago by • 0
0
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0
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64
views
supervised admixture
supervised admixture
20 hours ago by RT ▴ 10
0
votes
0
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59
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification Metagenomics Krona Kraken2
17 hours ago by Aytaç • 0
0
votes
0
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51
views
Trouble converting tfam and tped to map and ped files
plink ped tfam tped map
10 hours ago by Samantha • 0
0
votes
1
reply
50
views
Alignment of samples with spike-in
alignment multimapping RNA-seq ChIP-seq spike-in
updated 5 hours ago by 142k • written 5 hours ago by • 0
0
votes
0
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48
views
How to convert Haps file to vcf file?
pre-phasing GWAS imputation
7 hours ago by SeoGyun • 0
0
votes
0
replies
47
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA RNA-seq Nomalization Microarray
12 hours ago by jain72744 ▴ 10
0
votes
0
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46
views
input file in rmats
rmats
updated 8 hours ago by 11k • written 10 hours ago by • 0
0
votes
0
replies
46
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq imprinted 10x genes
12 hours ago by singcell • 0
0
votes
0
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42
views
How are score_weights calculated in this code?
cell single
6 hours ago by carolofharvest ▴ 40
0
votes
0
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22
views
Marker Features variance by cluster, sample, and treatment group
Seurat scATAC-seq features Marker ArchR
2 hours ago by naomiboldon • 0
93 results • Page 2 of 2
Recent Votes
Answer: Server or aws cloud- which one is better for gatk pipeline
Comment: Question about methylation location
Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
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Recent Replies
Answer: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
I've just displayed clipped bases and this is what it shows. Does this look right? ![enter image description here][1] ![enter imag…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Hi, I really appreciate you taking the time to reply. I'm still learning with IGV and sorry to sound very inexperienced but how would I che…
Answer: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
there is a clear shift in the depth just close to this mutation, you should set IGV to display the clipped bases + check if there is a DUP …
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message by Max • 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Giulio Genovese ▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Pierre Lindenbaum 161k
I think this is useless, in the gatk doc: > For each variant, the tool will look for the target coordinate, reverse-complement and left-al…
Comment: Too many unpaired forward reads found by Trimmomatic by GenoMax 142k
Ideally you will know which adapters to use but if you don't then programs like `fastp` can auto-detect them. You could also use `bbduk.sh`…
Comment: UMI-Tools knee-method has great influence on the results of white list by i.sudbery 19k
With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`. How…
Comment: samtools tview symbols by Ruqaiya • 0
What does the star mean then ?
Comment: RNA seq analysis by prifa ▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
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