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122,212 results • Page 701 of 2445
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4
votes
1
reply
1.5k
views
Reference Genome from NCBI BioProject ID or SRA
genome sequencing alignment software error
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 30
3
votes
7
replies
2.0k
views
[R, ShortRead] Subscript contains out-of-bounds indices
R
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 10
0
votes
0
replies
766
views
Any tool to mask specific probe sequence in an alignment bam file
bam masking probe
4.7 years ago by Ken ▴ 10
0
votes
0
replies
853
views
Issue with RGI heatmap
software error
updated 4.7 years ago by 20 • written 4.8 years ago by • 0
0
votes
3
replies
1.0k
views
Error occured in designing a matrix
R
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 30
0
votes
0
replies
676
views
mutation analysis, top mutations, maftools
gene
4.7 years ago by Rob ▴ 180
0
votes
11
replies
3.1k
views
Bowtie2: Mate file error & internal exception
alignment next-gen sequence
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
3
votes
8
replies
2.7k
views
Running snakemake on chromosomes in parallel
snakemake python vcf
updated 4.7 years ago by 166k • written 4.7 years ago by ▴ 10
0
votes
1
reply
876
views
Inter-tissue coexpression network analysis
correlation bipartite clustring coexpression
4.7 years ago by adR ▴ 130
1
vote
1
reply
4.4k
views
S4 Object data extraction in R
R S4
updated 4.7 years ago by 13k • written 4.7 years ago by • 0
0
votes
2
replies
4.5k
views
vcftool negative relatedness values for family members
vcftools kinship qc pedigree
updated 4.7 years ago by 20 • written 9.5 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Segmentation fault with HOMER
homer HiC
updated 3.9 years ago by • 0 • written 4.7 years ago by ★ 1.5k
0
votes
0
replies
827
views
A database of cancer super-enhancers
ChIP-Seq super-enhancers cancer
4.7 years ago by MoHallal • 0
2
votes
3
replies
4.4k
views
BCL2FASTQ Dual-Index Barcode Collisions - Is the i5 Index not considered when determining the number of mismatches?
bcl2fastq barcode collision barcode-mismatches
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 110
2
votes
10
replies
4.6k
views
Converting an Rdata set to an excel sheet
R Gene
updated 4.7 years ago by 13k • written 4.7 years ago by • 0
0
votes
0
replies
1.1k
views
whole length hg38 genomic repeat annotation file
RNA-Seq
4.7 years ago by dew ▴ 10
1
vote
1
reply
2.0k
views
Colour tip labels in a tree based on wildcard/expression using ggtree
ggtree colour R phylogeny dendrogram
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 30
0
votes
0
replies
682
views
Masses in topology files for coarse-grained molecular dynamics simulations
molecular dynamics topology simulation lipid
4.7 years ago by ballaneypranav • 0
2
votes
3
replies
2.2k
views
Renaming Fasta ID's according to their number and on specific string length
sequence
updated 4.7 years ago by 45k • written 8.8 years ago by • 0
4
votes
12
replies
2.5k
views
Dot-plot in R with different data sets.
R
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 90
5
votes
11
replies
2.9k
views
FASTQ File Comparison
sequencing genome
4.7 years ago by biohacker_tobe ▴ 80
0
votes
2
replies
970
views
Is mutation activating or inactivating?
mutation activating inactivating
updated 4.7 years ago by ▴ 300 • written 4.7 years ago by • 0
1
vote
1
reply
2.3k
views
VEP missing refseq annotation in refseq cache?
vep
updated 4.7 years ago by 24k • written 4.7 years ago by • 0
0
votes
2
replies
1.1k
views
Option -qcovs for tblastn
tblastn -qcovs blast option
4.7 years ago by melanie.m • 0
0
votes
1
reply
1.2k
views
Job: Bioinformatician to analyse clinical datasets - Faculty of Medical Sciences | Newcastle University, UK
variant-detection genomic-medicine
updated 2.3 years ago by 45k • written 4.7 years ago by • 0
0
votes
0
replies
500
views
WGCNA coexpression of deisased related module
R
4.7 years ago by mahmudaga • 0
0
votes
4
replies
1.4k
views
STAR alignment loop segmentation fualt (core dumped)
STAR
updated 2.5 years ago by 45k • written 4.7 years ago by • 0
0
votes
0
replies
668
views
Normalization step and use of package in differential junction expression analysis
RNA-Seq as junction-usage RJunBase ASJA
4.7 years ago by Elvira Nightingale • 0
2
votes
3
replies
8.0k
views
How to get fastq files of SRA in Galaxy
RNA-Seq next-gen sequencing
updated 4.7 years ago by ▴ 130 • written 4.7 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Edit the NCBI Taxonomy with ete3 toolkit ?
taxonomy taxdump ncbi ete3 toolkit
4.7 years ago by Pierre • 0
0
votes
3
replies
1.0k
views
Best way to download a subsection of a genome that matches a search query on NCBI's Blast?
blast ncbi alignment
4.7 years ago by Tom ▴ 20
2
votes
8
replies
2.8k
views
How to run Blastn on an input data with manual database?
ncbi+ blast
4.7 years ago by mthm ▴ 80
0
votes
2
replies
1.1k
views
Help in testing alligning this one RNA-seq data
rna-seq hisat2
4.6 years ago by qmarulfiz ▴ 60
1
vote
0
replies
1.1k
views
Job: Postdoc Fellowships - EMBL | Stanford Life Science Alliance
gene genome next-gen-sequencing rna-seq
updated 2.3 years ago by 45k • written 4.7 years ago by ▴ 10
2
votes
2
replies
1.1k
views
GEO2R script for analysing microarray data
R limma
4.7 years ago by raavi21198 ▴ 20
20
votes
7
replies
4.7k
views
6 follow
Why are we assuming genes are not differentially expressed?
rna-seq
4.7 years ago by greyman ▴ 190
0
votes
8
replies
3.0k
views
Different gen identifiers with the same gene name [HTA 2.0 microarrays]
HTA2.0 annotation microarrays
4.6 years ago by Hamtaro ▴ 60
1
vote
2
replies
1.5k
views
preprocess of the nanopore seqeucning data
nanopore cat fastq
updated 4.7 years ago by 48k • written 4.7 years ago by ▴ 80
1
vote
1
reply
1.2k
views
oma-cleanup cannot be executed
OMA
updated 4.7 years ago by ★ 1.1k • written 4.7 years ago by • 0
0
votes
0
replies
696
views
Proximity Extension Assay (PEA) technology
proteomics NPX
4.7 years ago by priyayadavaiims • 0
0
votes
0
replies
587
views
RNA-seq dataset search
RNA-Seq
4.7 years ago by ramyak1912 • 0
0
votes
1
reply
898
views
Meta-analyses "Error: No p-value field found in aa_results.assoc.linear."
snp
updated 3.5 years ago by • 0 • written 4.7 years ago by • 0
0
votes
0
replies
732
views
umap differential pattern of expression
Seurat scRNA-seq
4.7 years ago by LacquerHed ▴ 30
2
votes
2
replies
1.9k
views
Is differential gene expression coupled with differential transcript usage more informative than just differential transcript expression?
RNA-Seq R
4.7 years ago by peter.brockport ▴ 10
0
votes
2
replies
1.3k
views
Which is the best way to work with NCBI data obtaining online partial information from the whole
genbank r python
updated 4.7 years ago by 20 • written 6.6 years ago by • 0
2
votes
1
reply
1.0k
views
How to show statistical significance of overlap of CTCF binding sites
RNA-Seq genome
4.7 years ago by samuel ▴ 260
0
votes
0
replies
725
views
Filter multisample VCF for variants with less than N samples
VCF
4.7 years ago by bjwiley23 ▴ 40
0
votes
1
reply
1.0k
views
how to check significant differential methylation, hypermethylated or hypomethylated betweem case and control groups?
dna_methylation differential_methylation
4.7 years ago by carlos_marchi ▴ 90
9
votes
3
replies
4.3k
views
Question about Finding SRA IDs
software error genome sequencing
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 30
12
votes
5
replies
9.2k
views
Tool: AGAT - Another Gff/Gtf Analysis Toolkit
gff gtf
updated 2.4 years ago by 45k • written 5.9 years ago by 9.3k
122,212 results • Page 701 of 2445
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Recent Replies
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 ▴ 130
@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…
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…
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