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420 results • Page 3 of 9
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0
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3
replies
1.8k
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How to remove batch effect in copy number segment mean
Combat CNA Batch-Effect
updated 22 days ago by 43k • written 5.5 years ago by ▴ 150
3
votes
3
replies
233
views
Gene Specific coverage from WGS data
linux WGS Bioinformatics SARS CoV2
3 days ago by Adyasha • 0
0
votes
2
replies
300
views
RNAseq 1 control 2 different treatment
RNA-seq
24 days ago by matteo.levorato • 0
0
votes
2
replies
172
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression DEG model
11 days ago by Lluís R. ★ 1.2k
0
votes
2
replies
192
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression DESeq2
2 days ago by Nicholas • 0
0
votes
2
replies
290
views
Bedmethyl file format
bedmethyl methylation
updated 23 days ago by 142k • written 23 days ago by ▴ 20
0
votes
2
replies
102
views
LncRNA Nomenclature
ENST nomenclature lncrna GBB ENSG
10 hours ago by jain72744 ▴ 10
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios Cox-model survival
updated 23 days ago by 43k • written 4.4 years ago by ▴ 40
0
votes
2
replies
254
views
Downloading older version of a tool
Alignment tools
6 days ago by Ruqaiya • 0
2
votes
2
replies
221
views
Raw counts using stringtie
stringtie RNA-seq
updated 7 days ago by 142k • written 7 days ago by • 0
1
vote
2
replies
347
views
Extracting information from gff3 file produced by augustus
augustus gff3
updated 24 days ago by 100k • written 26 days ago by • 0
0
votes
2
replies
574
views
autodockvina
python python3 autodock
updated 21 days ago by 43k • written 4 months ago by • 0
1
vote
2
replies
269
views
permutation test in edgeR
rna-seq edgeR
updated 18 days ago by ★ 7.1k • written 4 weeks ago by • 0
0
votes
2
replies
418
views
How can I solve this error?
metal
22 days ago by 22211020193 • 0
1
vote
2
replies
243
views
Downloading full alignments from Pfam
pfam
5 days ago by bef1 • 0
1
vote
2
replies
248
views
convert a seurat object to expressionset
Seurat
29 days ago by Bine ▴ 60
0
votes
2
replies
293
views
VCF annotation with gnomADv4 using R package
annotation gnomADv4 R VCF
23 days ago by DKA ▴ 40
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 6 days ago by • 0 • written 10.2 years ago by ▴ 20
2
votes
2
replies
215
views
PDB related issue
rcsb pdb
updated 11 days ago by ▴ 580 • written 11 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
0
votes
2
replies
311
views
bam merging for archaic samples
samtools bam
updated 19 days ago by 43k • written 20 days ago by ▴ 100
1
vote
2
replies
304
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast pssm
9 days ago by Nafi • 0
0
votes
2
replies
244
views
How to detect and visualize ORFs in bacterial genome?
statistics visualization ORFs genome
28 days ago by marongiu.luigi ▴ 710
0
votes
2
replies
288
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics scRNA-seq proliferation
23 days ago by mropri ▴ 150
0
votes
2
replies
411
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
21 days ago by Ashok • 0
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 23 days ago by 43k • written 3.0 years ago by ▴ 60
0
votes
2
replies
161
views
Phasing a mixture of two individuals' DNA with long reads
long-reads phasing
2 days ago by njornet ▴ 20
0
votes
2
replies
461
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
21 days ago by _quantum_girl_ ▴ 10
0
votes
2
replies
456
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
21 days ago by Ashok • 0
0
votes
2
replies
295
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn Normalization RPKM TPM
27 days ago by ramin.k2013 • 0
0
votes
2
replies
236
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
3 days ago by Ahiad Chen Zion • 0
0
votes
2
replies
292
views
WGCNA
PCA WGCNA EIGENGENE
28 days ago by rajasekargutha ▴ 60
0
votes
2
replies
358
views
GSEA analysis in R
GSEA R Arabidopsis
22 days ago by Sudip • 0
0
votes
2
replies
296
views
Annovar using R package
Annovar gnomAD R
14 days ago by DKA ▴ 40
1
vote
2
replies
272
views
alignment result
RNA-seq samtools hisat2
15 days ago by ahmad.sajad4541 • 0
1
vote
2
replies
232
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana gtf reference-genome
updated 10 days ago by 43k • written 10 days ago by • 0
0
votes
2
replies
326
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK PANDAS R
23 days ago by Koketso • 0
2
votes
2
replies
640
views
Batch correction for DE analysis
batch-correction mRNA RNA-seq DEGs MDSplot
updated 23 days ago by 43k • written 2.7 years ago by ▴ 10
2
votes
2
replies
324
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 15 days ago by 43k • written 16 days ago by ▴ 140
1
vote
2
replies
268
views
POSSUM not working due to incompatible pssm file
fasta pse-pssm pssm POSSUM
8 days ago by rianna.collins • 0
0
votes
2
replies
203
views
Differentail gene expression results
differential expression gene rna-seq Deseq2
updated 2 days ago by 14k • written 3 days ago by • 0
1
vote
2
replies
315
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 23 days ago by 43k • written 23 days ago by • 0
0
votes
2
replies
208
views
Base Quality Score Recalibration with different reference genome
SNPs GATK BQSR RNA-seq
7 days ago by dtnondorf • 0
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
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 23 days ago by 43k • written 4.4 years ago by ▴ 10
1
vote
2
replies
312
views
Tumour purity and ploidy estimation
Copy-number Whole-exome-sequencing
24 days ago by bp22 ▴ 80
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma RNA-Seq edgeR batch-effect
updated 21 days ago by 43k • written 7.0 years ago by • 0
0
votes
2
replies
218
views
What should I consider as FASTA for dataset?
PDB FASTA
10 days ago by Nafi • 0
1
vote
2
replies
822
views
What type of normalization does removeBatchEffect function require as the input?
batch limma removeBatchEffect rna-seq batch-effect
updated 23 days ago by 43k • written 21 months ago by ▴ 20
0
votes
2
replies
579
views
How to get the reference panel for UKBB
UKBB GWAS clump
21 days ago by 航太郎 • 0
420 results • Page 3 of 9
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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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