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186 results • Page 1 of 4
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0
votes
4
replies
47
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
21 minutes ago by Tuck898 • 0
0
votes
0
replies
25
views
Marker Features variance by cluster, sample, and treatment group
Seurat scATAC-seq features Marker ArchR
2 hours ago by naomiboldon • 0
0
votes
3
replies
73
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
1
vote
7
replies
445
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 5 hours ago by 161k • written 3 days ago by • 0
0
votes
5
replies
125
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
1 hour ago by SilhouetteQ • 0
0
votes
1
reply
53
views
Alignment of samples with spike-in
alignment multimapping RNA-seq ChIP-seq spike-in
updated 6 hours ago by 142k • written 6 hours ago by • 0
0
votes
0
replies
44
views
How are score_weights calculated in this code?
cell single
6 hours ago by carolofharvest ▴ 40
0
votes
0
replies
49
views
How to convert Haps file to vcf file?
pre-phasing GWAS imputation
8 hours ago by SeoGyun • 0
2
votes
12
replies
2.7k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 days ago by • 0 • written 4.8 years ago by ▴ 60
0
votes
0
replies
52
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
82
views
Microbial Signal Transduction Database
MiST
updated 8 hours ago by 11k • written 11 hours ago by • 0
0
votes
0
replies
47
views
input file in rmats
rmats
updated 8 hours ago by 11k • written 11 hours ago by • 0
0
votes
1
reply
94
views
DESeq2 error
DESeq2
updated 11 hours ago by 82k • written 14 hours ago by ▴ 20
0
votes
0
replies
47
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
1
reply
104
views
When should I use R-MarkDown over R-Script ?
r rscript rmarkdown
updated 9 hours ago by 82k • written 12 hours ago by ▴ 160
0
votes
2
replies
102
views
LncRNA Nomenclature
ENST nomenclature lncrna GBB ENSG
10 hours ago by jain72744 ▴ 10
0
votes
0
replies
48
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA RNA-seq Nomalization Microarray
13 hours ago by jain72744 ▴ 10
5
votes
2
replies
108
views
EdgeR - relationship between logFC and coefficients
differential-expression r edger
updated 12 hours ago by ★ 7.1k • written 14 hours ago by ▴ 10
2
votes
5
replies
266
views
Importing a fastq file
Fastq
updated 14 hours ago by ▴ 120 • written 1 day ago by • 0
3
votes
1
reply
87
views
Question about methylation location
Methylation WGBS bisulfide
updated 5 hours ago by ★ 1.9k • written 17 hours ago by • 0
0
votes
0
replies
60
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification Metagenomics Krona Kraken2
18 hours ago by Aytaç • 0
0
votes
0
replies
68
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
votes
0
replies
66
views
supervised admixture
supervised admixture
20 hours ago by RT ▴ 10
0
votes
0
replies
69
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization Mendelian two-sample
22 hours ago by Nikki • 0
2
votes
0
replies
69
views
News: course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics SNPs LocalAdaptation GIS
23 hours ago by carlopecoraro2 ★ 2.5k
0
votes
8
replies
313
views
Different output for read length
samtools BAM
21 hours ago by marco.barr ▴ 100
0
votes
1
reply
286
views
Snakemake fails to find conda in PBS
snakemake
updated 1 day ago by ▴ 60 • written 28 days ago by • 0
0
votes
2
replies
139
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 1 day ago by 142k • written 1 day ago by • 0
2
votes
3
replies
163
views
Truncated metadata file report from ENA Portal API
ena python
updated 6 hours ago by 142k • written 1 day ago by • 0
0
votes
0
replies
74
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
replies
481
views
JASPAR2024_getMatrixSet error
JASPAR2024 getMatrixSet
updated 1 day ago by 43k • written 11 weeks ago by ▴ 10
0
votes
3
replies
161
views
How to convert normalized BigWig file to count matrix?
count-matrix BigWig
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
3
replies
213
views
bcftools - reducing to "sites-only"?
sites-only bcftools
updated 1 day ago by 161k • written 1 day ago by • 0
0
votes
1
reply
102
views
input file for alternative splicing in rmats in linux
rmats
updated 1 day ago by 43k • written 1 day ago by • 0
1
vote
2
replies
179
views
Server or aws cloud- which one is better for gatk pipeline
aws server calling gatk cloud
updated 1 day ago by 54k • written 1 day ago by ▴ 20
1
vote
1
reply
408
views
ComBat_Seq stuck adjusting the data
Batch-Effect RNAseq ComBat-Seq
updated 1 day ago by • 0 • written 4 months ago by ▴ 10
4
votes
3
replies
2.6k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq picard validatesamfile
updated 1 day ago by 161k • written 1 day ago by ★ 1.2k
2
votes
3
replies
174
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 1 day ago by 161k • written 1 day ago by ▴ 10
1
vote
0
replies
104
views
What is Deepvariant default filtering values ?
vcf calling filter variant deepvariant
1 day ago by Shae ▴ 10
0
votes
1
reply
159
views
Enhanced Volcano-Cut off
foldchange enhancedvolcano
updated 1 day ago by ▴ 100 • written 1 day ago by ▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 1 day ago by 142k • written 3.2 years ago by ▴ 10
1
vote
1
reply
126
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
1
vote
2
replies
1.6k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring SCTransform Seurat
updated 1 day ago by • 0 • written 2.3 years ago by ▴ 10
0
votes
0
replies
101
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
106
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
3
replies
226
views
Contig assembly task, errors
genetics contig assembly dna bioinformatics
updated 15 hours ago by 8.4k • written 1 day ago by • 0
1
vote
3
replies
215
views
Help with Biopython for Beginner
Python ORF FASTA Biopython
updated 1 day ago by 142k • written 1 day ago by • 0
0
votes
0
replies
112
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep vcf gnomad
1 day ago by asalimih ▴ 60
0
votes
2
replies
229
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 1 day ago by 19k • written 1 day ago by • 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 1 day ago by • 0 • written 5.7 years ago by ▴ 30
186 results • Page 1 of 4
Recent Votes
Comment: samtools tview symbols
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
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Recent Replies
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Ah I've just found 'show soft clipped bases' and this is what comes up... how come it is all greyed out? ![enter image description here][…
Comment: 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…
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