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122,217 results • Page 717 of 2445
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RNA-seq DEGs downstream analysis and reporting in literature
RNA-Seq gene R
updated 4.8 years ago by 22k • written 4.8 years ago by ▴ 20
0
votes
0
replies
400
views
Export Large deepSNV File
next-gen snp
4.8 years ago by arno • 0
29
votes
16
replies
41k
views
7 follow
What Is A "Lane" In Next Generation Sequencing Context?
sequencing
updated 4.8 years ago by ▴ 30 • written 13.4 years ago by ▴ 410
0
votes
0
replies
796
views
comparative genomics BPGA
genome gene
4.8 years ago by glady ▴ 320
2
votes
7
replies
1.3k
views
Speed up the blast option remove.
blast online
updated 4.8 years ago by 11k • written 4.8 years ago by ▴ 40
3
votes
2
replies
2.3k
views
Pyranges: obtaining sets of overlaps or overlap pairs
pyranges overlaps overlap pairs List overlaps
updated 4.8 years ago by 36k • written 4.8 years ago by ▴ 50
0
votes
0
replies
810
views
Help with GISTIC results
GISTIC
4.8 years ago by zizigolu ★ 4.4k
3
votes
4
replies
1.9k
views
htseq-count returns 0 count for all
RNA-Seq htseq-count
updated 23 months ago by 16k • written 4.8 years ago by ▴ 10
2
votes
3
replies
1.2k
views
Help with analyzing NCBI tissue expression data - solr xml file
solr ncbi tissue expression xml RNA-Seq
4.8 years ago by j.matt.franklin • 0
2
votes
0
replies
2.9k
views
deepSplit=2 vs deepSplit=4
gene WGCNA Coexpression R
updated 4.8 years ago by 20 • written 4.9 years ago by ▴ 30
2
votes
0
replies
2.9k
views
recommended minimum cell numbers to pseudobulk for DE comparisons between groups
RNA-Seq scRNA single-cell
4.8 years ago by Sentinel156 ▴ 190
0
votes
0
replies
651
views
replicate analyses and divide snp subsetsin admixture
admixture subsets replicate
4.8 years ago by Daier ▴ 20
0
votes
0
replies
741
views
replicate analyses in admixture
admixture replicate
4.8 years ago by Daier ▴ 20
1
vote
0
replies
1.3k
views
error unrecognized command line option fPIC
Compilation error mismatched makefile environment
updated 4.8 years ago by 45k • written 4.8 years ago by ▴ 90
0
votes
1
reply
861
views
gene ID conversion
RNA-Seq gene
updated 4.8 years ago by ▴ 90 • written 4.8 years ago by • 0
0
votes
2
replies
2.0k
views
Intron orders transcripts like encoded amino acid
mRNA amino-acid RNA-Seq intron transcript
updated 2.8 years ago by 45k • written 10.6 years ago by • 0
1
vote
5
replies
2.0k
views
bcf tools fixref error
snpflip bcftools topmed fixref imputation
updated 2.5 years ago by 45k • written 4.8 years ago by • 0
2
votes
1
reply
1.8k
views
samtools index error
alignment
updated 4.8 years ago by 166k • written 4.8 years ago by ▴ 70
0
votes
0
replies
1.3k
views
Job: Senior Bioinformatician for Oligonucleotide Therapeutics at AstraZeneca Gothenburg (Sweden)
oligonucleotides genomics
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 230
0
votes
0
replies
812
views
LD network plot using netGWAS
R snp ld
4.8 years ago by ziv_attia • 0
0
votes
0
replies
727
views
Bacterial RNA-SEQ Aligner Rockhopper
RNA-Seq
4.8 years ago by Sammy ▴ 30
2
votes
1
reply
1.2k
views
BAM FLAG mate unmappedand mate reverse strand
BAM
updated 4.8 years ago by 22k • written 4.8 years ago by ▴ 30
0
votes
0
replies
964
views
Why does KAAS use SBH for partial genomes?
orthology blast reciprocal best hit annotation
4.8 years ago by Dunois ★ 2.9k
0
votes
2
replies
2.0k
views
antiSMASH error problem
genome gene
updated 4.8 years ago by 45k • written 4.8 years ago by ▴ 320
4
votes
7
replies
2.1k
views
Series matrix manual download now not supported (??)
GEO
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 50
1
vote
1
reply
3.4k
views
Interpreting nucleotide diversity
nucleotide diversity π SNP
updated 4.8 years ago by 20 • written 4.8 years ago by ▴ 50
1
vote
2
replies
1.5k
views
Number of upregulated and downregulated genes from counts matrix
RNA-Seq DEGs up and downregulated genes
4.8 years ago by taniamahmood38 ▴ 60
3
votes
3
replies
2.7k
views
Pyranges: operate on just metadata columns
pyranges pandas column selection
4.8 years ago by Bosberg ▴ 50
0
votes
0
replies
1.3k
views
Job: Post-doc position in multi-omics of Alzheimer's disease at Columbia University in New York City
post-doc multiomics GWAS R sequencing
updated 2.5 years ago by 45k • written 4.8 years ago by • 0
0
votes
1
reply
823
views
Bubble Plot of two different GO
Bubble Plot Gene Ontology
4.8 years ago by sb4158 • 0
0
votes
2
replies
1.1k
views
Chip_seq analysis remove duplicates
ChIP-Seq
4.8 years ago by luckysardar171 ▴ 20
1
vote
3
replies
1.7k
views
Suggested Trimmomatic inputs for LEADING and TAILING
RNA-Seq sequencing quality control
4.8 years ago by dadrasarmin ▴ 20
1
vote
6
replies
1.6k
views
RNASeq datasets with different total counts
normalization RNA-seq
updated 2.3 years ago by 45k • written 4.8 years ago by ▴ 120
3
votes
4
replies
2.0k
views
Blastn max target sequences
blastn ncbi
updated 4.8 years ago by ▴ 870 • written 4.8 years ago by • 0
1
vote
4
replies
4.9k
views
cellranger count error: No input FASTQs were found for the requested parameters.
scRNA cellranger
4.8 years ago by tiancaigg ▴ 30
4
votes
6
replies
1.8k
views
Forum: What are some areas of bioinformatics that are overdone?
bioinformatics
updated 2.7 years ago by 45k • written 4.8 years ago by 23k
1
vote
1
reply
1.9k
views
Read subgroup of HDF5 file with (0,0) group name?
hdf5 rhdf5 dataframe python pandas
updated 4.8 years ago by ★ 2.1k • written 5.4 years ago by ▴ 350
0
votes
1
reply
1.7k
views
FASTQ level UMI correction for TCR analysis
UMI fastq TCR RNA-Seq Mixcr
4.8 years ago by gordo2b ▴ 10
5
votes
5
replies
11k
views
how to remove duplicate SNP rows in vcf using bcftools norm
SNP
updated 4.8 years ago by ▴ 30 • written 5.8 years ago by ▴ 230
7
votes
11
replies
3.6k
views
Get top-contribution variant name for PCA result
R
4.8 years ago by luongthang1908 ▴ 50
1
vote
2
replies
854
views
miRNA seq, problems with alignment
RNA-Seq alignment
4.8 years ago by adrian.ramirezdearellano • 0
0
votes
0
replies
787
views
Canu 2.1.1 Storage issue at correction/1-overlapper
Assembly genome
4.8 years ago by arteen.marashi • 0
7
votes
11
replies
25k
views
11 follow
How to generate KEGG pathway classification chart
RNA-Seq kegg
updated 2.4 years ago by ▴ 20 • written 6.7 years ago by ▴ 30
0
votes
0
replies
1.8k
views
Basic questions about Ngsplot heatmaps
ngsplot heatmap
4.8 years ago by Aspire ▴ 390
0
votes
0
replies
804
views
Enrichr Diseases/Drugs Terms Explanation Help
enrichr rare-disease gene-list
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 40
2
votes
3
replies
1.9k
views
NO FDR <0.05 in the whole dataset
R RNA-Seq FDR qvalue
updated 4.8 years ago by 13k • written 4.8 years ago by ▴ 160
0
votes
2
replies
744
views
Selecting Samples based on Clustering
RNA-Seq sequencing gene
4.8 years ago by Hyper_Odin ▴ 320
3
votes
7
replies
2.1k
views
Has anyone heard the term data warehousing in genomics before?
data warehouse
updated 4.8 years ago by • 0 • written 7.0 years ago by ▴ 10
0
votes
5
replies
1.9k
views
how to debug error in RnBeads Mac mini 10.15.7 R 4.0.3
R Rnbeads debug bug illuminia
4.8 years ago by saba_nasir111 • 0
0
votes
6
replies
1.4k
views
how to find genes whose expressions are likely affected by interaction at any time in edgeR?
edgeR
4.8 years ago by calvin99 • 0
122,217 results • Page 717 of 2445
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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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