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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
2
votes
5
replies
1.9k
views
6 follow
Samtools Failing to Install through Conda
samtools
conda
updated 7 days ago by
Ram
40k • written 17 months ago by
jjp55
▴ 20
3
votes
11
replies
554
views
Should I Learn Docker to Run Command Line Bioinformatics Tool?
Docker
updated 23 hours ago by
Yogi
▴ 40 • written 8 days ago by
arriyaz.nstu
▴ 30
0
votes
1
reply
169
views
GO analysis after DESeq2
GO
updated 8 days ago by
Ram
40k • written 8 days ago by
oduduabasi.isaiah
• 0
3
votes
2
replies
204
views
Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
methylation
DMR
updated 7 days ago by
Basti
★ 1.7k • written 8 days ago by
epianalysis
• 0
0
votes
0
replies
114
views
News:
New NCBI Datasets APIs to Replace Old Ones
NCBI
API
Datasets
8 days ago by
PeterC_NCBI
▴ 330
1
vote
3
replies
254
views
miRDeep2 - identifying miRNAs from deep sequencing data
microRNA
miRDeep2
updated 8 days ago by
Ram
40k • written 8 days ago by
Hasan
• 0
3
votes
4
replies
232
views
Unable to build applet in DNAnexus, .jar file not found
dnanexus
applet
updated 8 days ago by
LChart
3.4k • written 8 days ago by
_quantum_girl_
▴ 10
1
vote
4
replies
300
views
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
ggplot2
ANOVA
t-test
7 days ago by
RM123
▴ 10
0
votes
1
reply
154
views
Download an example of fully-imputed VCF files ?
VCF
impute
updated 7 days ago by
barslmn
★ 1.9k • written 8 days ago by
Ben
• 0
0
votes
1
reply
174
views
How to find the most representative protein data base ID for your protein?
modelling
protein
database
updated 8 days ago by
GenoMax
135k • written 8 days ago by
amy__
▴ 150
0
votes
2
replies
202
views
Visualize where kmers are on a reference genome
kmer
visualize
updated 8 days ago by
Alex Reynolds
35k • written 8 days ago by
Carrie
• 0
7
votes
7
replies
404
views
Filter human transcription factors
transcription-factor
RNA-seq
updated 7 days ago by
jared.andrews07
★ 15k • written 8 days ago by
Chris
▴ 200
2
votes
6
replies
321
views
obtaining circular RNAs' sequences from circBase
circular-RNA
6 days ago by
aminijavad4
▴ 10
0
votes
0
replies
127
views
How to annotate BED for tissue expression?
BED
annotation
8 days ago by
Fabio_bie88
• 0
2
votes
0
replies
170
views
Job:
Human Genomics Team Leader
ebi
ensembl
embl
genomics
8 days ago by
Ben_Ensembl
★ 2.3k
0
votes
1
reply
1.7k
views
error when running local chlorop1.1
chlorop
updated 8 days ago by
Ram
40k • written 7.3 years ago by
gerrychang1985
▴ 40
3
votes
14
replies
1.9k
views
10 follow
Help writing code for a question on my homework
biopython
updated 6 days ago by
Joe
21k • written 2.4 years ago by
hannahcheyenna
• 0
1
vote
1
reply
240
views
bedGraph for Coverage of Insert from Paired-End Data?
genome
awk
coverage
bed
paired-end
updated 8 days ago by
shelkmike
▴ 980 • written 11 days ago by
vanbelj
▴ 40
0
votes
6
replies
293
views
gene correlations in between two groups
gene-expression
correlation
7 days ago by
biology_inform
▴ 40
0
votes
1
reply
129
views
Running Ibex on both BCR chains?
BCR
ibex
single-cell
updated 8 days ago by
Ram
40k • written 8 days ago by
actinia94
• 0
2
votes
9
replies
525
views
Calculation of TMB on gene level
genomics
updated 7 days ago by
svp
▴ 590 • written 8 days ago by
smrutimayipanda
▴ 20
0
votes
0
replies
118
views
Spike-in normalization in ATAC-Seq with DiffBind
ATAC-Seq
spike-in
DiffBind
8 days ago by
frueher
• 0
1
vote
2
replies
166
views
Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)
regress_out
Cell_cycle
Seurat
8 days ago by
alwayshope
▴ 30
1
vote
9
replies
409
views
how to identify uniq genes between two gff files.
Genes
Uniq
Annotation
GFF
6 days ago by
nikhil
▴ 20
1
vote
3
replies
449
views
I have performed Trimmomatic run for adapter removal. QC report shows drop in the reads and presence of overrepresented sequences. Seeking help!
NGS
bioinformatics
illumina
WGS
updated 8 days ago by
swbarnes2
13k • written 8 days ago by
Vijith
▴ 30
0
votes
0
replies
121
views
filtering variants in a Strelka2 VCF file based on AD and AF
Filter
VCF
8 days ago by
Bogdan
★ 1.4k
2
votes
4
replies
284
views
Integrated Seurat object change name of the two conditions
R
integrated
Seurat
8 days ago by
camillab.
▴ 140
0
votes
4
replies
357
views
Hugo_Symbol to Entrez ID
hugo
bioinformatics
entrez
ids
symbols
updated 9 days ago by
Kevin Blighe
86k • written 10 days ago by
shakyaram079
• 0
2
votes
5
replies
321
views
How to change from gene_id to GeneID/EntrezID using R
identifiers
Deseq2
GeneID
updated 8 days ago by
Kevin Blighe
86k • written 10 days ago by
Nicolas
• 0
0
votes
4
replies
741
views
Is there a way to get a list of all homogygous sites for each sample with plink (regardless if they are in a run)
plink
updated 9 days ago by
chrchang523
10k • written 24 days ago by
curious
▴ 730
1
vote
4
replies
275
views
How to sort cd-hit-est cluster file
sort
cd-hit-est
8 days ago by
Mo
▴ 40
1
vote
5
replies
309
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
7 days ago by
omer.shomrat
• 0
13
votes
10
replies
685
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 8 days ago by
ATpoint
77k • written 11 days ago by
MVJ
▴ 10
3
votes
4
replies
312
views
Dotplot : how to self-define the range of legend
analysis
seq
RNA
updated 8 days ago by
GenoMax
135k • written 9 days ago by
Xuhao
• 0
0
votes
0
replies
117
views
News:
RADseq data analysis course
RADseq
Phylogenomics
Bioinformatics
Populationgenomics
Stacks
9 days ago by
carlopecoraro2
★ 2.4k
3
votes
2
replies
393
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
9 days ago by
Thomas
▴ 20
0
votes
1
reply
215
views
Merging the filename with tsv files for master file
genomics
updated 7 days ago by
barslmn
★ 1.9k • written 10 days ago by
smrutimayipanda
▴ 20
4
votes
6
replies
396
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
updated 6 days ago by
Istvan Albert
98k • written 10 days ago by
Athena
• 0
2
votes
4
replies
371
views
Ties in reranked list
fgsea
GSEA
10 days ago by
Hamza
• 0
1
vote
5
replies
509
views
Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempting To Use CuffDiff
CuffDiff
Bash
Cufflinks
4 days ago by
Y
• 0
0
votes
0
replies
159
views
My rMATS output file is not showing gene symbols and only XLOC gene ID are being shown.
rMATS
rMATS-turbo
10 days ago by
Nipan
• 0
2
votes
4
replies
317
views
Using STAR aligner to build index of hg38
hg38
STAR
alignment
RNAseq
index
9 days ago by
Grace
• 0
0
votes
0
replies
164
views
Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values
bioinformatics
TPM
RNASeqV2
cbioportal
RSEM
updated 10 days ago by
4galaxy77
2.8k • written 10 days ago by
shakyaram079
• 0
0
votes
2
replies
285
views
Modify the code to take most abundant reads from a cluster and process it.
cd-hit-est
clustering
10 days ago by
Mo
▴ 40
1
vote
2
replies
270
views
Understanding TCGA barcodes with dot in the fieldname
tcga
updated 8 days ago by
Zhenyu Zhang
▴ 980 • written 11 days ago by
Tahsin
• 0
0
votes
0
replies
164
views
Compare peaks between clusters in sc-ATAC
Peak-Calling
Epigenome
scATAC-seq
updated 11 days ago by
Ram
40k • written 11 days ago by
Ahmed.waraky
▴ 10
1
vote
3
replies
374
views
How to DESeq2 using miRNA data obtained using TCGAbiolinks
R
TCGAbiolinks
DESeq2
TCGA
updated 11 days ago by
Zhenyu Zhang
▴ 980 • written 13 days ago by
Mo
• 0
0
votes
7
replies
541
views
Highly inflated p-values in GWAS by regenie
regenie
plink
gwas
9 days ago by
cwwong13
▴ 20
1
vote
3
replies
294
views
How to find out what adapters to remove after FastQC of RNAseq data?
Trimmomatic
FastQC
NGS
RNA-seq
8 days ago by
ella
• 0
2
votes
5
replies
361
views
Trimmomatic .jar not included anymore?
trimmomatic
ubuntu
linux
updated 11 days ago by
petebio
▴ 100 • written 11 days ago by
Emily
▴ 30
1,000 results • Page
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Answer: tensorQTL interaction issue
Answer: Script for getting summary statistic of any genome using GTF or GFF3 ?
Comment: How do you validate and verify your pipeline's software updates?
Comment: How do you validate and verify your pipeline's software updates?
Answer: GSEA with GO and KEGG datasets
GSEA with GO and KEGG datasets
Answer: Exporting DEGs obtained from DESeq2
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Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
Kevin Blighe
86k
It is difficult for me to comment, as I am not too informed on your IT infrastructure. What I can say is that it would be better to run the…
Answer: Converting from BED to SAF/GFF
by
alejandrogzi
▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Comment: Convert bed12 to GFF
by
alejandrogzi
▴ 30
Now there is [bed2gff](https://github.com/alejandrogzi/bed2gff), if you want to work only with a gff file!
Comment: Converting different annotation file formats (GTF/GFF/BED) to each other
by
alejandrogzi
▴ 30
now there is also [bed2gff](https://github.com/alejandrogzi/bed2gff) if you want to convert .bed files to .gff3 files!
Answer: How Do I Convert From Bed Format To Gff Format?
by
alejandrogzi
▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Answer: tensorQTL interaction issue
by
Solal
• 0
Writing a solution for anyone interested. The issue stems from a dosage error, some variant contains only heterozygous individuals and no h…
Answer: The Biostar Handbook. A bioinformatics e-book for beginners.
by
Qboy
• 0
Great book! I love using it to help my mentees to learn bioinformatics better. It would be also fantastic to compile all other necessary Pr…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Thanks. I'll try.
Comment: How to get sample names and genotype for SNP in multi-sample VCF file
by
avelarbio46
▴ 30
Hi! I'm trying to parallelize your code (to run on a bunch of files), but it is not working because of multiple processes spawning. Do you …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
> so I don't think the genome size is available. Perhaps not for your specific strain but plenty of other Kpn genomes are available and th…
Comment: Kimura% of calcDivergenceFromAlign output
by
睿紘
• 0
For additional information, "Coverage for each repeat class and divergence (Kimura)" is also the result from calcDivergenceFromAlign.pl
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
By the way, I run Rockhopper on the untrimmed files, and the full match percentage grew to 20%-30%, and there are 1552 transcripts in the u…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
langziv
▴ 50
Here are the total bases in 4 fastq files (after adapter removal): 1,027,852,411, 1,041,895,083, 1,121,786,520, 1,299,721,929. I just rem…
Comment: Understanding mother and father alleles in VCF file
by
c.
• 0
actually they didn't tell me which relatives were from mother side and which from father side, you are right. But how can you find related …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads
by
GenoMax
135k
Correct. Data that went into the assembly.
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