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122,217 results • Page 716 of 2445
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3
votes
9
replies
5.9k
views
6 follow
Multiple ensembl gene ID for the same gene name (Symbol), how to deal with this while differential analysis?
RNA-Seq alignment next-gen ensembl
updated 3.6 years ago by ▴ 10 • written 4.8 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Web-based tool for 3D visualization of proteins given a .pbd file
protein 3D structure prediction
4.8 years ago by giusdalt95 ▴ 10
3
votes
8
replies
2.4k
views
How to find the secreted protein tags
RNA-Seq protein rna-seq R next-gen
updated 4.8 years ago by ★ 2.4k • written 4.8 years ago by ▴ 70
0
votes
4
replies
1.3k
views
How to solve the problem related to unmatched chromosome identifiers?
RNA-Seq
updated 4.8 years ago by 20 • written 4.9 years ago by ▴ 10
1
vote
0
replies
808
views
Compare the output of two MEME analyses
meme motif analysis
4.8 years ago by lessismore ★ 1.4k
4
votes
3
replies
914
views
Remove a row if two specific columns have similar/share contents
SNP next-gen
4.8 years ago by waqasnayab ▴ 250
1
vote
2
replies
909
views
question regarding QC of scRNA-seq data
scRNA-seq scRNA-seq QC
4.8 years ago by Alex V. Gopanenko • 0
0
votes
11
replies
2.7k
views
The pruned in file by bcftools gives error "Wrong VCF header" while calculating kinship matrix using Rvtests
software error
4.8 years ago by AVA ▴ 40
2
votes
3
replies
1.3k
views
Affymatrix microarray data do not have normal distribution after normalization (left skewed)
microarray R
updated 4.8 years ago by ★ 90k • written 4.8 years ago by ▴ 30
16
votes
11
replies
2.8k
views
10 follow
Forum: Suggest common programming tasks for biologists who are novice programmers
education
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 40
4
votes
3
replies
4.5k
views
counting after aligning miRNA reads to miRBase mature miRNA instead of reference genome
miRNA-seq
updated 4.8 years ago by ▴ 160 • written 7.7 years ago by ▴ 30
0
votes
0
replies
623
views
Can I differenciate between two variants of the same plant spicies with NGS?
snp genome
4.8 years ago by jomagrax ▴ 40
1
vote
4
replies
1.0k
views
question regarding histone and lncRNA genes in poly(A) RNA-seq data
rna-seq polyA rna-seq
4.8 years ago by Alex V. Gopanenko • 0
1
vote
11
replies
5.0k
views
How to get REF and ALT alleles from a genotype data?
snp genome R sequencing
updated 4.8 years ago by 24k • written 4.8 years ago by ▴ 10
0
votes
0
replies
635
views
Horizontal sub-windows for IGV
IGV bam
4.8 years ago by German.M.Demidov ★ 3.0k
1
vote
6
replies
1.2k
views
How can I locate a specific nucleotide based on a bam file?
alignment genome sequence
4.8 years ago by 2689563392 • 0
1
vote
4
replies
3.1k
views
LImma design matrix and contrast matrix creation
R limma gordon smyth
updated 4.8 years ago by ★ 2.1k • written 4.8 years ago by ▴ 10
0
votes
1
reply
952
views
error in processing Agilent two channel microarray raw data
microarray
updated 4.8 years ago by ★ 8.6k • written 4.8 years ago by ▴ 30
1
vote
1
reply
1.5k
views
interaction analysis of smallRNA-seq and RNA-seq data
srnaRNA-se RNA-Seq
updated 4.8 years ago by 20 • written 7.6 years ago by ▴ 150
3
votes
2
replies
1.4k
views
Retrieve initial query in getBM()
getBM biomaRt R gene
updated 19 months ago by 45k • written 4.8 years ago by • 0
0
votes
5
replies
5.1k
views
Is there any method to convert a text file to VCF format?
SNP R gene next-gen
updated 17 months ago by 45k • written 4.8 years ago by ▴ 20
0
votes
0
replies
732
views
Variant splicing position on CDS
SNV
4.8 years ago by heureuse ▴ 10
5
votes
8
replies
1.8k
views
Does the countToFPKM package work for single end RNA seq or its only for paired end?
RNA-Seq
updated 4.8 years ago by 11k • written 4.8 years ago by ▴ 10
0
votes
0
replies
955
views
Comparation hmmer vs blast
hmmer Blast comparation
4.8 years ago by zion22 ▴ 70
0
votes
0
replies
961
views
Stacks: Denovo.pl M, m and n paramters
Assembly SNP RAD-Seq Stacks
4.8 years ago by virtualinterlect • 0
0
votes
9
replies
3.3k
views
BioPython local blast different results than blast+ local blast
blast biopython blast+ python
updated 4.8 years ago by 20 • written 7.4 years ago by • 0
0
votes
0
replies
888
views
Gene expression values each samples (replicates) using `AverageExpression` function
SEURAT SINGLE-CELL averageexpression
4.8 years ago by singcell ▴ 10
5
votes
2
replies
1.1k
views
Reorder "matrix" "array"
R
4.8 years ago by imrankhanbioinfo ▴ 70
0
votes
0
replies
960
views
Tumor mutation burden data
sequencing TCGA
4.8 years ago by wenbinm ▴ 40
0
votes
4
replies
1.8k
views
Cuffmerge Error: Converting GTF files to SAM
software error cufflinks cuffmerge
updated 4.8 years ago by 154k • written 4.8 years ago by • 0
1
vote
4
replies
1.7k
views
Forum: Very high ratio of cases to controls - how to increase statistical power?
gwas SNP
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 20
0
votes
1
reply
874
views
How a can extrac regions V3 and V4 of SILVA database 138?
sequencing rRNA
updated 4.8 years ago by 56k • written 4.8 years ago by • 0
2
votes
7
replies
3.9k
views
could not load index bfc tools af-dis plugin
bcftools vcf af-dist imputation
updated 2.5 years ago by 45k • written 4.8 years ago by • 0
3
votes
6
replies
7.5k
views
How To Trim An Arb Reference Database To A Specific 16S Region
database trimming phylogenetics metagenomics
updated 4.8 years ago by • 0 • written 12.6 years ago by ▴ 170
0
votes
0
replies
1.1k
views
Filtering vcf with dbSNP
dbSNP filter bcftools
updated 4.8 years ago by 20 • written 4.8 years ago by ▴ 60
0
votes
0
replies
717
views
p-adjusted threshold in pathfindR
pathfindR pathway-enrichment-analysis
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 80
1
vote
4
replies
1.5k
views
Forum: is valid to apply several cut offs thresholds to a data-matrix used to perform coexpression analysis until reach the desire result?
RNA-Seq matrix-filtering coexpression-analysis
updated 2.7 years ago by 45k • written 4.8 years ago by • 0
0
votes
0
replies
617
views
comparative genomic analysis of phages
BACTERIOPHAGES PhamDB ANI Comparative genomics
4.8 years ago by 4mumumu • 0
2
votes
1
reply
1.0k
views
I want to create a box plot for RNA-Seq data, but i am new to R, so i don't know, how to perform this task
RNA-Seq R
4.8 years ago by rishav513 ▴ 30
1
vote
1
reply
1.5k
views
UK biobank exome filtering
exome UKbiobank
updated 4.5 years ago by • 0 • written 4.8 years ago by ★ 1.0k
0
votes
0
replies
893
views
Extract monophyletic subtree with ETE3 toolkit
ETE3 python3
4.8 years ago by arunprasanna83 ▴ 60
2
votes
8
replies
3.7k
views
Lanes in the context of RNA-SEQ data
RNA-Seq
updated 4.8 years ago by 154k • written 4.8 years ago by ▴ 30
0
votes
0
replies
1.2k
views
Cancer Cell Line Encyclopedia (CCLE) raw dose response data
drug-response ccle gene drug-sensitivity
updated 2.4 years ago by 45k • written 4.8 years ago by • 0
0
votes
0
replies
1.1k
views
How to do differential CNA analysis?
CNA GISTIC Differential analysis
4.8 years ago by Raheleh ▴ 260
0
votes
2
replies
3.0k
views
Barplot: error Warning message: Removed rows containing missing values (geom_bar).
R
updated 4.8 years ago by 13k • written 4.8 years ago by • 0
3
votes
3
replies
1.5k
views
how to use unix tools to convert VCF genotypes like '1|1' to this '2'
bcftools unix
updated 2.5 years ago by 45k • written 4.8 years ago by ▴ 900
0
votes
0
replies
725
views
Suggestions for analyze dN, dS rate and omega (dN/dS ratio) result?
sequence gene
updated 4.8 years ago by 154k • written 4.8 years ago by • 0
3
votes
3
replies
6.1k
views
Mapping GRCh38 to ENSEMBL / UCSC ,Gene, transcript , cDNA and Protein IDs and Sequence
RNA-Seq SNP genome Mappping ENSEMBL
updated 4.8 years ago by 20 • written 8.8 years ago by ▴ 110
1
vote
4
replies
1.1k
views
How to match data from file 2 on 1st with deleting unmatched data
SNP gene sequence
4.8 years ago by shubhamkumbhar420 ▴ 40
1
vote
0
replies
1.0k
views
Parameter setting of NGSadmix
NGSadmix
4.8 years ago by Daier ▴ 20
122,217 results • Page 716 of 2445
Recent Votes
Comment: circos plot for genomic features
Answer: How to perform GO enrichment in non-model organisms?
Comment: circos plot for genomic features
Answer: How excactly is the Q30 is calculated?
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
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Recent Replies
Comment: Question about QC and scrublet by Arup Ghosh 3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms? by lieven.sterck 16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
Comment: circos plot for genomic features by Matteo Ungaro ▴ 140
@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
Comment: circos plot for genomic features by colindaven 8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated? by colindaven 8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
Answer: How excactly is the Q30 is calculated? by GenoMax 154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
Comment: best practice for diploid variant calling by Matteo Ungaro ▴ 140
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind by ATpoint 90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
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 ▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: 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 ▴ 10
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…
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