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97,217 results • Page 1 of 1945
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3
votes
6
replies
256
views
Adapter content in FASTQ file
Adapter FASTQC
14 minutes ago by shivangi.agarwal800 ▴ 70
0
votes
0
replies
12
views
Phasing variants in the middle generation (of three generations)
bioinformatics genomics genetics
updated 10 minutes ago by 110k • written 26 minutes ago by • 0
0
votes
0
replies
17
views
Job: Ph.D. Bioinformatics Specialist (Long-Term Contract) - NIH/NIEHS - Research Triangle Park, NC
NGS bioinformatics scRNA-seq
55 minutes ago by Susan • 0
0
votes
1
reply
33
views
BEDOPS bedmap confusing file for option
BEDOPS Methylation bedmap
updated 20 minutes ago by 110k • written 2 hours ago by • 0
0
votes
0
replies
13
views
Diploma thesis
thesis genomic student
1 hour ago by novakovas647 • 0
0
votes
0
replies
11
views
Get UniProt GO terms in R
UniProt R Gene Ontology term GO
1 hour ago by Space_Life ▴ 20
0
votes
2
replies
49
views
Using IndexFeatureFile to index vcf
GATK
1 hour ago by shpak.max • 0
0
votes
1
reply
24
views
Dropseq, GSE124872 and structure of the reads in the FastQ files
scRNA-seq Dropseq
updated 1 hour ago by 11k • written 2 hours ago by ▴ 10
0
votes
0
replies
19
views
Removing stop codons in alignment using hyphy
hyphy alignment
2 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
44
views
Tutorial: TCGA transcriptome data to R (DESeq2)
DESeq2 TCGA GDC
3 hours ago by Barry Digby ▴ 790
1
vote
0
replies
87
views
Isolate contrasts using DESeq2 when use a combination of categorical and continuous variables
DESeq2 contrast design
4 hours ago by tiansy ▴ 10
0
votes
0
replies
33
views
Adding repeats in a genome fasta at a particular location without messing up the annotations?
genomics repeats annotation
5 hours ago by hchetia • 0
0
votes
1
reply
50
views
how do you get an IN-FRAME deletion stop gain variant?
genomics annotation ensembl VEP genetics
5 hours ago by jon.klonowski ▴ 80
0
votes
0
replies
44
views
Job: Ph.D. Programs in Bioinformatics and Multi-omics Research
PhD student positions
5 hours ago by lid • 0
0
votes
0
replies
45
views
Using simple t-test for selected genes of the microarray dataset
gene expression microarray t-test
updated 6 hours ago by 55k • written 10 hours ago by ★ 1.5k
0
votes
1
reply
63
views
Error "start too small" when running htseq-count on a sorted .bam file
htseq-count htseq
updated 3 hours ago by 11k • written 6 hours ago by • 0
0
votes
1
reply
81
views
Getting errors trying to run rmats
analysis splicing rMATs
updated 6 hours ago by • 0 • written 8 hours ago by • 0
0
votes
3
replies
138
views
calculate percentage of bases covered by the transcriptome
coverage granges
updated 7 hours ago by 110k • written 9 hours ago by ▴ 10
0
votes
1
reply
71
views
RNAEditingIndexer
RNA edit
updated 8 hours ago by ★ 6.4k • written 8 hours ago by ▴ 10
0
votes
1
reply
283
views
Group comparison of CNA between primary and metastatic samples
sequencing genome
updated 8 hours ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
83
views
Add or reveal read groups on .sam file aligned by BWA
gatk haplotypecaller
updated 8 hours ago by 90k • written 12 hours ago by • 0
2
votes
6
replies
237
views
Run multiple times samtools and sed for a big number of bam files in folder
samtools bash bam
updated 3 hours ago by 6.5k • written 12 hours ago by ▴ 30
1
vote
2
replies
137
views
need some help on how to use DESeq2 for TCGA data
DESeq2 TCGA R TCGA-Assembler
updated 6 hours ago by ★ 1.9k • written 13 hours ago by • 0
0
votes
9
replies
744
views
Alignments not labelled as proper pair on bwa mem
software error
updated 1 hour ago by 110k • written 18 months ago by • 0
0
votes
0
replies
60
views
Job: Postdoc (3 years) in Bioinformatics and 3D genome modeling
hi-c bioinformatics genomics ngs next-gen
12 hours ago by jonas.paulsen • 0
0
votes
7
replies
212
views
How do I put the color scales on heatmap.2?
heatmap.2 colorscale margins
updated 8 hours ago by 17k • written 12 hours ago by • 0
0
votes
0
replies
35
views
Customise Waterfall plot in GenVisR
mutation GenVisR waterfall R genomic
12 hours ago by isd1989 • 0
0
votes
0
replies
50
views
How to reintroduce sample divisions to a metagenomic co-assembly, what are the best practices?
coverage assembly metagenomic
12 hours ago by robert.murphy ▴ 60
0
votes
1
reply
92
views
How to find gene annotation given a position in a bacterial genome
position annotation snp intergenic
updated 56 minutes ago by 33k • written 1 day ago by • 0
0
votes
1
reply
80
views
Convert Log2 (FPKM+0.001) to FPKM in an expression matrix obtained from TCGA
RNA-Seq TCGA RSEM
updated 13 hours ago by ★ 2.3k • written 13 hours ago by • 0
0
votes
0
replies
47
views
Finding science projects or researchers
projects researcher freelance collaboration
13 hours ago by Anastasiya M • 0
0
votes
0
replies
33
views
correlation coefficient for node degree distribution
correlation coefficient cytoscape
14 hours ago by imaparna27 • 0
0
votes
1
reply
145
views
How to describe bi-plot PCA figure?
PCA
updated 15 hours ago by ★ 15k • written 16 hours ago by ▴ 20
0
votes
0
replies
66
views
Error with hicdcdiff function in HiCDCPlus package
hi-chip R hicdcplus deseq2 differential interactions
16 hours ago by koushik.vf09 ▴ 20
0
votes
0
replies
79
views
how to visually compare BAM file differences
mutation tumor GATK bam somatic
17 hours ago by tan • 0
1
vote
1
reply
295
views
High Number of Unassigned Reads in MEGAN?
diamond megan metagenomics
updated 17 hours ago by • 0 • written 4 months ago by ▴ 10
2
votes
1
reply
409
views
How to understand Structural Variation in bedpe format?
SV bedpe
updated 18 hours ago by • 0 • written 12 months ago by ★ 8.8k
0
votes
1
reply
105
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 13 hours ago by ★ 2.3k • written 19 hours ago by ▴ 60
0
votes
3
replies
190
views
Including tbi file along with VCF when running VEP on remote dataset (GnomadV3)
VCF VEP gnomad annotation
updated 2 hours ago by ▴ 260 • written 21 hours ago by ▴ 190
8
votes
3
replies
210
views
Fq file to table
convert Fq
updated 13 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 23 hours 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
23 hours ago by xinmiaoyan28 • 0
0
votes
3
replies
205
views
How to determine the cut off threshold when removing the RNA-Seq with low variance?
analysis RNA sequence gene
updated 13 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
94
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
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
CPM function in EDGER
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Recent Replies
Answer: 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)
Answer: how do you get an IN-FRAME deletion stop gain variant? by jon.klonowski ▴ 80
I think I can see it. It is when the deletion causes the bases to fall back in place such that the a stop codon is generated but technicall…
Comment: need some help on how to use DESeq2 for TCGA data by Hamid Ghaedi ★ 1.9k
In this [repository][1], I provide R code to download bladder cancer data from TCGA (TCGA-BLCA) using the package `TCGABiolinks` and then …
Answer: Getting errors trying to run rmats by patrickdm • 0
Hello, the last error message > File "/N/soft/rhel7/rmats/4.0.2/rMATS-turbo-Linux-UCS2/rmats.py", line 31 print "mapping the first sample"…
Comment: Applying Machine Learning on vcf file by curious ▴ 630
in NA10831 and NA19109 it looks like the deletion spans most the length of cyp2d6 and breaks just before the start of cyp2d7. This is proba…
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