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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
4
votes
18
replies
4.1k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 20 months ago by
Ram
43k • written 8.4 years ago by
Joel TM
▴ 60
5
votes
18
replies
6.7k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
4.4 years ago by
michelle.piquet
▴ 60
3
votes
18
replies
3.2k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 2.8 years ago by
Ram
43k • written 2.8 years ago by
Nai
▴ 50
14
votes
18
replies
4.9k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 7.3 years ago by
Biostar
20 • written 7.5 years ago by
plink_9857
▴ 50
14
votes
18
replies
2.2k
views
Clustering in single cell
seurat
single-cell
updated 6 months ago by
e.r.zakiev
▴ 200 • written 6 months ago by
Chris
▴ 260
7
votes
18
replies
4.9k
views
Fold change UP and Down in dplyr calculation
R
6.7 years ago by
1769mkc
★ 1.2k
7
votes
18
replies
8.6k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
hana
▴ 190
16
votes
18
replies
5.4k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.7 years ago by
Mensur Dlakic
★ 27k • written 4.7 years ago by
tikshyadav19
• 0
3
votes
18
replies
1.9k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
18 months ago by
lacb
▴ 120
20
votes
17
replies
6.0k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
6.7 years ago by
Anand Rao
▴ 630
7
votes
17
replies
4.3k
views
Strange MA-plot using DESeq2
rna-seq
R
deseq2
updated 7.3 years ago by
Biostar
20 • written 7.4 years ago by
stan
▴ 80
5
votes
17
replies
4.3k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics
encode
10.1 years ago by
14134125465346445
★ 3.6k
5
votes
17
replies
8.5k
views
Removing fastq duplicates
sequence
next-gen
ChIP-Seq
3.4 years ago by
C4
▴ 30
28
votes
17
replies
22k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.4 years ago by
Leite
★ 1.3k
0
votes
17
replies
1.5k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
3.6 years ago by
Dunois
★ 2.5k
12
votes
17
replies
4.9k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
6.5 years ago by
anonymous1192976466
▴ 50
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.5 years ago by
dimitrischat
▴ 210
2
votes
17
replies
9.6k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping
genome
fastq
STAR
updated 2.1 years ago by
todd.ugine
• 0 • written 3.3 years ago by
merfer0206
• 0
7
votes
17
replies
3.9k
views
How to find the differences in aligned bam files
RNA-Seq
7.1 years ago by
1769mkc
★ 1.2k
4
votes
17
replies
2.8k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray
gene-expression
CV
error
4.8 years ago by
Jurat Shahidin
▴ 100
0
votes
17
replies
4.9k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 19 months ago by
Ram
43k • written 8.6 years ago by
jigarnt
▴ 30
2
votes
17
replies
2.9k
views
Snakemake Megahit error
megahit
Snakemake
2.4 years ago by
blackadder
▴ 30
6
votes
17
replies
2.4k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen
assembly
genome
alignment
5.8 years ago by
williamsbrian5064
▴ 510
2
votes
17
replies
4.4k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam
bam
alignment
samtools
updated 10.3 years ago by
Devon Ryan
104k • written 10.3 years ago by
Rohit
★ 1.5k
0
votes
17
replies
2.7k
views
Fail running blastdb and blastn on my own computer
blast
6.5 years ago by
annette440
• 0
20
votes
17
replies
3.2k
views
How to add "transcript" feature to a gtf file?
gtf
updated 9 months ago by
1769mkc
★ 1.2k • written 3.2 years ago by
pomodoro_sinensis
▴ 110
0
votes
17
replies
1.1k
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
3 months ago by
Foad
▴ 10
9
votes
17
replies
2.2k
views
Creating intergenic bam file
R
genome
intergenic
alignment
7.7 years ago by
erincyurtman
• 0
4
votes
17
replies
2.8k
views
Cufflinks analysis and gffread
RNA-Seq
Assembly
updated 6.5 years ago by
Kevin Blighe
87k • written 6.5 years ago by
qudrat
▴ 100
8
votes
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools
relatedness
6.2 years ago by
Sharon
▴ 600
3
votes
17
replies
2.8k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing
faire
mapping
3.1 years ago by
boczniak767
▴ 850
7
votes
17
replies
6.5k
views
HeatMap: how to cluster only the rows and keep order of the heatmap's column labels as same as in the df?
R
gene
genome
5.8 years ago by
WUSCHEL
▴ 750
0
votes
17
replies
3.6k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq
wgcna
software error
R
next-gen
updated 2.3 years ago by
Dio
• 0 • written 5.6 years ago by
giuseppe0525
▴ 20
1
vote
17
replies
2.4k
views
Normalizing BLAST results
blast
updated 6.6 years ago by
Biostar
20 • written 6.7 years ago by
db
• 0
0
votes
17
replies
3.0k
views
I am not able to let R read my file
R
fasta
updated 3.1 years ago by
Arup Ghosh
3.2k • written 3.1 years ago by
trejomarco6
• 0
3
votes
17
replies
1.5k
views
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV
DownSample
fastq
copy number not accurate
4.2 years ago by
lffu_0032
▴ 90
1
vote
17
replies
4.2k
views
Error executing bedops convert2bed
bedops
bed
vcf
convert2bed
7.3 years ago by
lakhujanivijay
5.8k
2
votes
17
replies
5.1k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 6.1 years ago by
h.mon
35k • written 6.1 years ago by
Janey
▴ 30
1
vote
17
replies
5.7k
views
BBMap: Mapping Fails
BBTools
BBMap
Mapping
updated 8.1 years ago by
GenoMax
141k • written 8.1 years ago by
cacampbell
▴ 60
7
votes
16
replies
3.6k
views
How do I get a GFF file
snp
4.8 years ago by
apl00028
▴ 90
0
votes
16
replies
4.6k
views
Issue using MaSuRCA-3.2.6
Assembly
assembler
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
Chvatil
▴ 130
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 10 months ago by
Ram
43k • written 4.2 years ago by
Ankit
▴ 500
3
votes
16
replies
3.5k
views
FastTree trifurcating Root node
alignment
FastTree
Phylogenetic Tree
5.3 years ago by
Moses
▴ 150
2
votes
16
replies
3.1k
views
Enhancing draft genome using 10X data
10X
draft_genome
Assembly
5.7 years ago by
Mostafa
▴ 20
7
votes
16
replies
2.8k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq
sequencing
updated 13 months ago by
Ram
43k • written 6.5 years ago by
Matteo Schiavinato
★ 3.6k
5
votes
16
replies
2.6k
views
a lot of OTUs wth no reference
16S
6.5 years ago by
agata88
▴ 870
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene
next-gen
4.3 years ago by
Chaimaa
▴ 260
9
votes
16
replies
1.9k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
5.5 years ago by
bioinfo456
▴ 150
4
votes
16
replies
943
views
hisat2 location does not exist
hisat2
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Eric
• 0
0
votes
16
replies
4.3k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 21 months ago by
Ram
43k • written 9.0 years ago by
bharata1803
▴ 560
1,000 results • Page
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Answer: Seurat merge and batch correction
Answer: Seurat merge and batch correction
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
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Comment: How to compare the quality of assemblies
by
kirillkirilenko
▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024
by
geneontologyhelp
▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
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