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122,217 results • Page 721 of 2445
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767
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whole genome sequence -meta analysis
next-gen gwas gcta genome
4.8 years ago by Neu ▴ 10
0
votes
3
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1.7k
views
What object in GEO2R R code environment to use for ggplot2 Volcano and listing DEG?
GEO2R R bioconductor array
updated 4.6 years ago by ▴ 290 • written 4.8 years ago by ▴ 60
14
votes
4
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7.8k
views
A question regarding log2 transformation in EdgeR
EdgeR log2 differentail expression analysis
updated 4.8 years ago by ★ 8.6k • written 4.8 years ago by ▴ 300
4
votes
1
reply
2.7k
views
does anyone knows how to Create a presence absence heatmap like this?
R gene
updated 4.8 years ago by ★ 19k • written 4.8 years ago by • 0
2
votes
4
replies
1.2k
views
Subtracting FASTAs to get unique sequences?
alignment sequence FASTA subtraction
updated 4.8 years ago by ★ 30k • written 4.8 years ago by • 0
0
votes
9
replies
1.7k
views
Help on local alignment. Is there any way to automate the process?
NCBI OTU metabarcoding next-gen alignment
updated 4.8 years ago by 20 • written 4.8 years ago by • 0
1
vote
1
reply
1.1k
views
blastx diamond returns taxid "NA" for some sequence queries
blastx diamond taxonomy
4.8 years ago by pedrorodrigues ▴ 10
0
votes
2
replies
936
views
Amplicon variant calling from PacBio CCS reads
sequencing SNP
updated 4.8 years ago by 154k • written 4.8 years ago by ▴ 20
0
votes
3
replies
1.2k
views
vcf file column name error
sequencing
updated 4.8 years ago by 166k • written 4.8 years ago by • 0
4
votes
7
replies
1.7k
views
DESeq multiple factor question
R RNA-Seq sequencing differential-expression
updated 4.8 years ago by 9.0k • written 4.8 years ago by ▴ 20
1
vote
11
replies
3.6k
views
GATK HaplotypeCaller Error
software error rna-seq gatk
4.8 years ago by sahar.salimi92 • 0
0
votes
0
replies
555
views
How to remove NAs from mset object in MetaboAnalystR
r mummichog metabolystr
4.8 years ago by lewhiteside ▴ 10
0
votes
0
replies
1.3k
views
Job: Division Safety Coordinator at Berkeley Lab in Berkeley, CA
safety biosciences
updated 2.5 years ago by 45k • written 4.8 years ago by ▴ 70
0
votes
4
replies
2.7k
views
Snakemake aggregate input from rule with wildcards
snakemake
updated 4.8 years ago by 23k • written 4.8 years ago by • 0
1
vote
5
replies
1.7k
views
Cell type assignment for non-model organism single cell RNA-seq
RNA-Seq scRNA-Seq single cell non-model organism
4.8 years ago by predeus ★ 2.1k
1
vote
4
replies
1.4k
views
Heatmap of top 20 genes
RNA-Seq
updated 4.8 years ago by 45k • written 4.8 years ago by • 0
0
votes
0
replies
730
views
designing primers from CIRI2 output
RNA-Seq circRNA validation
updated 4.8 years ago by 20 • written 4.9 years ago by • 0
4
votes
8
replies
2.1k
views
COG database merger python code update (part-2)
python COG database
4.8 years ago by MSRS ▴ 590
0
votes
0
replies
686
views
How can I efficiently visualize ribosome positions?
Ribo-seq RNA-Seq rna-seq R NGS
4.8 years ago by taufiqbge • 0
6
votes
10
replies
3.9k
views
Running blastp locally though the NCBI nr dabase taking is weeks to run.
assembly
4.8 years ago by Bacteria_forever ▴ 10
4
votes
8
replies
2.1k
views
Extracting the Best sequence per genomic region in a genome based on the Best e-value
genome e-value parsing
updated 3.7 years ago by 45k • written 4.8 years ago by ▴ 20
1
vote
5
replies
1.8k
views
Human WGS :which genome reference
genome alignment reference
updated 4.8 years ago by 90k • written 4.8 years ago by ▴ 120
0
votes
1
reply
1.2k
views
Experience with BaseRecalibratorSpark and ApplyBQSRSpark
gatk somatic mutations snp
updated 4.8 years ago by 8.1k • written 4.8 years ago by ▴ 420
0
votes
0
replies
1.1k
views
Job: PhD / Post-doc position: Computational Epigenomics (Saarbruecken, Germany)
phd epigenomics
updated 2.5 years ago by 45k • written 4.8 years ago by ▴ 50
4
votes
2
replies
1.7k
views
Merging chip-seq samples sequenced in two different runs
ChIP-Seq RNA-Seq
updated 4.8 years ago by 9.0k • written 4.8 years ago by ▴ 70
2
votes
5
replies
1.5k
views
Error in Saving Files
python PDB
updated 4.8 years ago by 20 • written 4.8 years ago by ▴ 140
3
votes
2
replies
1.5k
views
Is it necessary to test for multiple correction during differential expression analysis on microRNA data?
microRNA miRNA-seq differential expression stats
updated 4.8 years ago by 9.0k • written 4.8 years ago by ▴ 150
0
votes
3
replies
3.6k
views
FASTQC - Good "Per Base Sequence Quality" but Bad "Per Tile Sequence Quality"?
fastqc covid-19 ngs
4.8 years ago by cg1440 ▴ 60
0
votes
2
replies
1.5k
views
RNA-seq spike-ins with Drosophila cells
RNA-Seq spike-ins
4.8 years ago by theodore ▴ 130
0
votes
10
replies
5.8k
views
Imputing missing genotypes using Beagle
Beagle missing
4.8 years ago by marinamartinezalvaro • 0
4
votes
7
replies
6.8k
views
Beagle imputation - duplication position error
SNP
updated 4.8 years ago by • 0 • written 7.5 years ago by ▴ 30
7
votes
6
replies
2.6k
views
nohup with while loop
bash loop SRAtoolkit
4.8 years ago by pt.taklifi ▴ 70
0
votes
2
replies
1.6k
views
Large majority of RNASeq reads mapping to intergenic regions - common issues excluded
rna-seq alignment STAR htseq
4.8 years ago by npb27 ▴ 20
3
votes
3
replies
880
views
Problems sam > bam conversion
sequencing alignment genome
4.8 years ago by Pinca ▴ 10
1
vote
3
replies
1.2k
views
SRA runs: How should I know which run is control and which one is treatment?
RNA-Seq
updated 4.8 years ago by ▴ 10 • written 4.8 years ago by ▴ 10
0
votes
1
reply
1.1k
views
compare two assembly genomes
assembly pangenome
updated 4.8 years ago by ▴ 590 • written 4.8 years ago by ▴ 10
3
votes
7
replies
2.5k
views
lncRNA quantification using featureCounts
lncRNA featureCounts
4.8 years ago by kuntalasb ▴ 10
2
votes
2
replies
1.8k
views
COG database download error (part-1)
cog annotation ftp
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 590
2
votes
4
replies
3.2k
views
CIBERSORT: Errors were encountered in input files, run aborted:
deconvolution cibersort
updated 2.7 years ago by 45k • written 4.8 years ago by ★ 4.5k
6
votes
6
replies
2.7k
views
gzip: uniprot_sprot_human.dat.gz: not in gzip format
gunzip error linux ubuntu unzip
4.8 years ago by Sashinika • 0
6
votes
8
replies
7.2k
views
[mem_sam_pe] paired reads have different names. Without -p
bwa alignment next-gen
updated 4.8 years ago by ★ 4.5k • written 7.8 years ago by ▴ 20
3
votes
5
replies
3.1k
views
How to parse protein and dna sequences from prokka generated gbk or gff file based on locus_tag?
genome perl python bash R
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 120
4
votes
3
replies
2.5k
views
kraken2 no longer supported? - NCBI downloads no longer working
alignment
4.8 years ago by susan.klein ▴ 30
0
votes
3
replies
3.2k
views
Kallisto: Estimated average fragment length
RNA-Seq alignment next-gen sequencing
4.8 years ago by jayeshkumarsundaram ▴ 10
2
votes
1
reply
928
views
How can I download all ncbi genomes files from a given country?
Assembly genome ncbi
updated 4.8 years ago by ★ 1.7k • written 4.8 years ago by • 0
1
vote
0
replies
2.0k
views
Job: Two Research Scientist Positions
Genomics Computational-Biology
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 10
0
votes
1
reply
2.5k
views
module membership p-value cutoff
wgcna module membership p-value cutoff
updated 4.8 years ago by 20 • written 8.2 years ago by ▴ 530
2
votes
1
reply
1.3k
views
detection of inverted repeats of transposons in Bacteria
sequence transposon inverted repeats
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 60
0
votes
1
reply
1.1k
views
Job: Biochemist Postdoc Fellow at Berkeley Lab in Berkeley, CA
SAXS SIBYLS
updated 2.5 years ago by 45k • written 4.8 years ago by ▴ 70
0
votes
0
replies
1.0k
views
WGCNA package for R - Gene coexpression analysis
WGCNA coexpression RNA-Seq dendrograme R
4.8 years ago by sofiablancoglez • 0
122,217 results • Page 721 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: Issue while running Kenddata. by GenoMax 154k
Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
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…
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