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97,217 results • Page 1 of 1945
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Diploma thesis
thesis genomic student
updated 1 hour ago by ★ 15k • written 3 hours ago by • 0
3
votes
7
replies
290
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Adapter content in FASTQ file
Adapter FASTQC
2 hours ago by shivangi.agarwal800 ▴ 70
0
votes
0
replies
24
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Phasing variants in the middle generation (of three generations)
bioinformatics genomics genetics
updated 2 hours ago by 110k • written 2 hours ago by • 0
0
votes
0
replies
42
views
Job: Ph.D. Bioinformatics Specialist (Long-Term Contract) - NIH/NIEHS - Research Triangle Park, NC
NGS bioinformatics scRNA-seq
3 hours ago by Susan • 0
0
votes
1
reply
66
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BEDOPS bedmap confusing file for option
BEDOPS Methylation bedmap
updated 2 hours ago by 110k • written 4 hours ago by • 0
0
votes
0
replies
28
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Get UniProt GO terms in R
UniProt R Gene Ontology term GO
3 hours ago by Space_Life ▴ 20
0
votes
2
replies
84
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Using IndexFeatureFile to index vcf
GATK
3 hours ago by shpak.max • 0
0
votes
1
reply
60
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Dropseq, GSE124872 and structure of the reads in the FastQ files
scRNA-seq Dropseq
updated 3 hours ago by 11k • written 4 hours ago by ▴ 10
0
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0
replies
32
views
Removing stop codons in alignment using hyphy
hyphy alignment
4 hours ago by el97004 ▴ 40
633
votes
159
replies
74k
views
95 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook tutorial training News
updated 22 days ago by 360 • written 5.0 years ago by 90k
0
votes
0
replies
56
views
Tutorial: TCGA transcriptome data to R (DESeq2)
DESeq2 TCGA GDC
5 hours ago by Barry Digby ▴ 790
1
vote
0
replies
94
views
Isolate contrasts using DESeq2 when use a combination of categorical and continuous variables
DESeq2 contrast design
6 hours ago by tiansy ▴ 10
0
votes
0
replies
39
views
Adding repeats in a genome fasta at a particular location without messing up the annotations?
genomics repeats annotation
7 hours ago by hchetia • 0
0
votes
1
reply
58
views
how do you get an IN-FRAME deletion stop gain variant?
genomics annotation ensembl VEP genetics
7 hours ago by jon.klonowski ▴ 80
0
votes
0
replies
54
views
Job: Ph.D. Programs in Bioinformatics and Multi-omics Research
PhD student positions
7 hours ago by lid • 0
0
votes
0
replies
48
views
Using simple t-test for selected genes of the microarray dataset
gene expression microarray t-test
updated 8 hours ago by 55k • written 12 hours ago by ★ 1.5k
0
votes
1
reply
75
views
Error "start too small" when running htseq-count on a sorted .bam file
htseq-count htseq
updated 5 hours ago by 11k • written 8 hours ago by • 0
0
votes
1
reply
89
views
Getting errors trying to run rmats
analysis splicing rMATs
updated 8 hours ago by • 0 • written 10 hours ago by • 0
0
votes
3
replies
150
views
calculate percentage of bases covered by the transcriptome
coverage granges
updated 9 hours ago by 110k • written 12 hours ago by ▴ 10
0
votes
1
reply
79
views
RNAEditingIndexer
RNA edit
updated 10 hours ago by ★ 6.4k • written 10 hours ago by ▴ 10
0
votes
1
reply
290
views
Group comparison of CNA between primary and metastatic samples
sequencing genome
updated 10 hours ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
85
views
Add or reveal read groups on .sam file aligned by BWA
gatk haplotypecaller
updated 11 hours ago by 90k • written 15 hours ago by • 0
2
votes
6
replies
256
views
Run multiple times samtools and sed for a big number of bam files in folder
samtools bash bam
updated 5 hours ago by 6.5k • written 14 hours ago by ▴ 30
1
vote
2
replies
153
views
need some help on how to use DESeq2 for TCGA data
DESeq2 TCGA R TCGA-Assembler
updated 8 hours ago by ★ 1.9k • written 15 hours ago by • 0
0
votes
9
replies
761
views
Alignments not labelled as proper pair on bwa mem
software error
updated 3 hours ago by 110k • written 18 months ago by • 0
0
votes
0
replies
62
views
Job: Postdoc (3 years) in Bioinformatics and 3D genome modeling
hi-c bioinformatics genomics ngs next-gen
14 hours ago by jonas.paulsen • 0
0
votes
7
replies
217
views
How do I put the color scales on heatmap.2?
heatmap.2 colorscale margins
updated 10 hours ago by 17k • written 14 hours ago by • 0
0
votes
0
replies
39
views
Customise Waterfall plot in GenVisR
mutation GenVisR waterfall R genomic
14 hours ago by isd1989 • 0
0
votes
0
replies
52
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How to reintroduce sample divisions to a metagenomic co-assembly, what are the best practices?
coverage assembly metagenomic
14 hours ago by robert.murphy ▴ 60
0
votes
1
reply
93
views
How to find gene annotation given a position in a bacterial genome
position annotation snp intergenic
updated 2 hours ago by 33k • written 1 day ago by • 0
0
votes
1
reply
83
views
Convert Log2 (FPKM+0.001) to FPKM in an expression matrix obtained from TCGA
RNA-Seq TCGA RSEM
updated 15 hours ago by ★ 2.3k • written 15 hours ago by • 0
0
votes
0
replies
49
views
Finding science projects or researchers
projects researcher freelance collaboration
15 hours ago by Anastasiya M • 0
0
votes
0
replies
34
views
correlation coefficient for node degree distribution
correlation coefficient cytoscape
16 hours ago by imaparna27 • 0
0
votes
1
reply
150
views
How to describe bi-plot PCA figure?
PCA
updated 17 hours ago by ★ 15k • written 19 hours ago by ▴ 20
0
votes
0
replies
70
views
Error with hicdcdiff function in HiCDCPlus package
hi-chip R hicdcplus deseq2 differential interactions
18 hours ago by koushik.vf09 ▴ 20
0
votes
0
replies
79
views
how to visually compare BAM file differences
mutation tumor GATK bam somatic
19 hours ago by tan • 0
1
vote
1
reply
298
views
High Number of Unassigned Reads in MEGAN?
diamond megan metagenomics
updated 20 hours ago by • 0 • written 4 months ago by ▴ 10
2
votes
1
reply
412
views
How to understand Structural Variation in bedpe format?
SV bedpe
updated 21 hours ago by • 0 • written 12 months ago by ★ 8.8k
0
votes
1
reply
110
views
Map mouse RNA-seq Ensembl gene ids to "org.Mm.eg.db", but get some "UNKNOWN" gene symbol, like "NA..25729", is it normal?
DEseq2 rna-seq DEG
updated 15 hours ago by ★ 2.3k • written 21 hours ago by ▴ 60
0
votes
3
replies
203
views
Including tbi file along with VCF when running VEP on remote dataset (GnomadV3)
VCF VEP gnomad annotation
updated 4 hours ago by ▴ 260 • written 23 hours ago by ▴ 190
8
votes
3
replies
212
views
Fq file to table
convert Fq
updated 15 hours ago by 33k • written 1 day ago by ▴ 10
0
votes
3
replies
192
views
API for retrieving genes' sequences from genes' symbols in a single call
gene-sequence linux API gene-symbol
updated 1 day ago by 33k • written 1 day ago by ▴ 20
0
votes
0
replies
46
views
How to prepare the markers file for GISTIC CNVkit analysis based on WES data
data analysis GISTIC cnv WES
1 day ago by xinmiaoyan28 • 0
0
votes
3
replies
206
views
How to determine the cut off threshold when removing the RNA-Seq with low variance?
analysis RNA sequence gene
updated 15 hours ago by 55k • written 1 day ago by • 0
0
votes
1
reply
114
views
What is the best way to load bgen files into python?
BGEN Python
updated 1 day ago by ▴ 510 • written 1 day ago by • 0
0
votes
0
replies
45
views
Mean samples coverage and mapping quality in Qualimap
mapping coverage quality Qualimap
1 day ago by Eli • 0
0
votes
1
reply
95
views
Fastest pipeline for large scale joint genotype calling?
calling
updated 1 day ago by 140k • written 1 day ago by ▴ 60
2
votes
3
replies
190
views
Are adapter sequences trimmed from ONLY the 3' ends of reads
RNA-SEQ
1 day ago by Pei ▴ 130
0
votes
1
reply
114
views
scaffold vs chromosome level assembly
assembly chromosom scaffold
updated 1 day ago by 50k • written 1 day ago by ▴ 110
0
votes
1
reply
117
views
How to directly perform enrichment analysis on GO ID
r
updated 1 day ago by 90k • written 1 day ago by • 0
97,217 results • Page 1 of 1945
Recent Votes
A: What is a count matrix for input into Seurat supposed to look like?
WGCNA::cor namespace issue
WGCNA::cor namespace issue
A: Changing names of Fasta headers
How to identify TSS sites from bacterial RNA-Seq data?
A: What Is The Difference Between Refseq And Ensembl Database?
Isolate contrasts using DESeq2 when use a combination of categorical and continuous variables
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Recent Replies
Comment: What is a count matrix for input into Seurat supposed to look like? by Pratik Mehta ▴ 700
Hey yea, you just need to have your cells as columns and your genes as rows. The "meat" of the data frame should be your counts. This shoul…
Answer: Diploma thesis by Mensur Dlakic ★ 15k
When I hear `diploma thesis`, I am thinking about an undergraduate student doing some kind of honors work that is not absolutely required f…
Comment: Adapter content in FASTQ file by opplatek ▴ 150
FastQC Sequence Length Distribution module is set to assume all your sequences should have the same length. You can ignore the red X since …
Comment: Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_ by opplatek ▴ 150
This solution worked for me. Just FYI, the vresion is not `v1.8.0`, but `v0.1.8` (rvcheck [versions][1]). I didn't check whether downgradin…
Comment: Adapter content in FASTQ file by shivangi.agarwal800 ▴ 70
Hi Guys, Thank you so much for the nice answers. I attempted to cut adapters via cutadapt using command below **cutadapt -a AGATCGGAA…
Answer: BEDOPS bedmap confusing file for option by Alex Reynolds 33k
After cleaning up the code, it looks like you are passing three files to `bedmap`, but it only takes two files: a reference file and a map …
Comment: Using IndexFeatureFile to index vcf by shpak.max • 0
Thanks. Is there anything analogous in GATK 3 that would create idx files?
Comment: Alignments not labelled as proper pair on bwa mem by GenoMax 110k
I see. Try aligning with bbmap and let us know if that helps. You could pre-merge the PE reads since they overlap using `bbmerge.sh` but I …
Comment: Dropseq, GSE124872 and structure of the reads in the FastQ files by swbarnes2 11k
Based on that single read alone, I'd be inclined to think that the first 20 bases are the cell barcode and UMI, and the stuff after the T's…
Answer: Using IndexFeatureFile to index vcf by Pierre Lindenbaum 140k
there no such tool in gatk3.8 java -jar gatk-3.8/GenomeAnalysisTK.jar -h 2>&1 | grep Index it looks like it exists in gatk4.* https:…
Comment: Including tbi file along with VCF when running VEP on remote dataset (GnomadV3) by Michal @Ensembl ▴ 260
Unfortunately, there's no way to point the VEP to a different dir, the tbi files have to be in the same directory.
Comment: Deseq2 dataframematrix error by swbarnes2 11k
You could also try feeding in truncated versions of the count data until you identify the offending row.
Comment: Error "start too small" when running htseq-count on a sorted .bam file by swbarnes2 11k
I'm not sure that a reference that includes haplotypes and patches is best for STAR: (emphasis original) > Generally, patches and alterna…
Comment: Run multiple times samtools and sed for a big number of bam files in folder by rpolicastro 6.5k
The sorting step is probably the slowest part, so multithreading it like you said with `-@` would greatly speed it up.
Comment: Run multiple times samtools and sed for a big number of bam files in folder by lieven.sterck 12k
it can I think, something weird-ish though, with an @ or such ? (can't recall the exact syntax now)
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