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112,609 results • Page
1 of 2253
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
14
views
Dotplot : how to self-define the range of legend
RNA
seq
analysis
1 hour ago by
Xuhao
• 0
0
votes
0
replies
44
views
How to change from gene_id to GeneID/EntrezID using R
identifiers
Deseq2
GeneID
6 hours ago by
Nicolas
• 0
0
votes
1
reply
72
views
Merging the filename with tsv files for master file
genomics
7 hours ago by
smrutimayipanda
▴ 20
0
votes
0
replies
49
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
9 hours ago by
Athena
• 0
2
votes
4
replies
240
views
Ties in reranked list
fgsea
GSEA
10 hours ago by
Hamza
• 0
762
votes
162
replies
122k
views
105 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 weeks ago by
Biostar
2.0k • written 6.8 years ago by
Istvan Albert
98k
1
vote
4
replies
204
views
Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempting To Use CuffDiff
CuffDiff
Bash
Cufflinks
11 hours ago by
Y
• 0
0
votes
0
replies
61
views
My rMATS output file is not showing gene symbols and only XLOC gene ID are being shown.
rMATS
rMATS-turbo
13 hours ago by
Nipan
• 0
1
vote
3
replies
141
views
Using STAR aligner to build index of hg38
hg38
STAR
alignment
RNAseq
index
updated 12 hours ago by
GenoMax
134k • written 14 hours ago by
Grace
• 0
0
votes
0
replies
83
views
Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values
bioinformatics
TPM
RNASeqV2
cbioportal
RSEM
updated 12 hours ago by
4galaxy77
2.8k • written 21 hours ago by
shakyaram079
• 0
0
votes
1
reply
213
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
updated 21 hours ago by
Christophe
• 0 • written 3 days ago by
Thomas
• 0
0
votes
3
replies
171
views
Hugo_Symbol to Entrez ID
hugo
bioinformatics
entrez
ids
symbols
updated 10 hours ago by
GenoMax
134k • written 1 day ago by
shakyaram079
• 0
0
votes
2
replies
186
views
Modify the code to take most abundant reads from a cluster and process it.
cd-hit-est
clustering
9 hours ago by
Mohd
▴ 40
0
votes
1
reply
122
views
Understanding TCGA barcodes with dot in the fieldname
tcga
updated 1 day ago by
Ram
40k • written 1 day ago by
Tahsin
• 0
0
votes
0
replies
92
views
Compare peaks between clusters in sc-ATAC
Peak-Calling
Epigenome
scATAC-seq
updated 1 day ago by
Ram
40k • written 1 day ago by
Ahmed.waraky
▴ 10
3
votes
7
replies
337
views
6 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 1 day ago by
Ram
40k • written 1 day ago by
MVJ
• 0
0
votes
0
replies
91
views
bedGraph for Coverage of Insert from Paired-End Data?
genome
awk
coverage
bed
paired-end
1 day ago by
vanbelj
▴ 40
1
vote
3
replies
288
views
How to DESeq2 using miRNA data obtained using TCGAbiolinks
R
TCGAbiolinks
DESeq2
TCGA
updated 1 day ago by
Zhenyu Zhang
▴ 980 • written 3 days ago by
Mo
• 0
0
votes
6
replies
330
views
Highly inflated p-values in GWAS by regenie
regenie
plink
gwas
updated 14 hours ago by
4galaxy77
2.8k • written 2 days ago by
cwwong13
▴ 20
1
vote
1
reply
140
views
How to find out what adapters to remove after FastQC of RNAseq data?
Trimmomatic
FastQC
NGS
RNA-seq
updated 1 day ago by
Ram
40k • written 1 day ago by
ella
• 0
2
votes
5
replies
245
views
Trimmomatic .jar not included anymore?
trimmomatic
ubuntu
linux
updated 1 day ago by
petebio
▴ 100 • written 1 day ago by
Emily
▴ 30
0
votes
1
reply
121
views
News:
EMBL-EBI virtual course | Introduction to RNA-seq and functional interpretation
RNA-seq
updated 1 day ago by
Ram
40k • written 1 day ago by
Rebecca
• 0
0
votes
4
replies
231
views
Weirdness in annotation (missing allele frequencies)
allele-frequency
gnomad
annovar
updated 7 hours ago by
Jeremy Leipzig
21k • written 1 day ago by
Can Abdullah
• 0
1
vote
3
replies
156
views
Finding sequences in unannotated genomes using reference coordinates
consensus
VCF
updated 1 day ago by
Ram
40k • written 1 day ago by
Prangan
▴ 20
0
votes
1
reply
149
views
High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq
RNA-seq
DNA
SMARTer
updated 1 day ago by
Ram
40k • written 1 day ago by
Mat
▴ 60
2
votes
2
replies
184
views
How to check RNAseq support for annotated genes?
gene
RNA-seq
annotation
updated 1 day ago by
Michael
53k • written 1 day ago by
BioinfoBee
• 0
0
votes
0
replies
142
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
R
GEO
GEOmetadb
updated 1 day ago by
Pierre Lindenbaum
157k • written 1 day ago by
nonaddldy
▴ 10
1
vote
0
replies
116
views
News:
Online Training - Bioinformatics Pipeline Development with Nextflow (November 15-17, 2023)
nextflow
automation
pipeline
development
1 day ago by
David Langenberger
10k
0
votes
3
replies
213
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 1 day ago by
Ram
40k • written 2 days ago by
vk
▴ 40
1
vote
1
reply
159
views
Simulate short-read RNA-seq data from long-read RNA-seq data
polyester
single-cell
simulation
short-read
long-read
updated 2 days ago by
Mensur Dlakic
★ 24k • written 2 days ago by
rhonddaskl
• 0
0
votes
0
replies
114
views
Gene enrichment analysis of prokaryotes gene
prokaryotes
GO
enrichment
DEG
2 days ago by
Genta
• 0
4
votes
4
replies
341
views
DESeq2 analysis using two featureCounts generated from different studies
RNA-seq
DESeq2
1 day ago by
abedkurdi10
▴ 190
3
votes
4
replies
271
views
Filtering VCF to divide with equal sizes
bcftools
vcf
updated 2 days ago by
Ram
40k • written 2 days ago by
avelarbio46
▴ 30
0
votes
0
replies
122
views
High pvalues when using clusterProfiler for seurat
clusterProfiler
2 days ago by
Ahmed
• 0
5
votes
2
replies
195
views
kallisto normalized TPM values without bootstraps
tpm
cibersort
sleuth
kallisto
RNA-seq
1 day ago by
butterman16
▴ 20
5
votes
7
replies
334
views
Salmon index not progressing
salmon
updated 1 day ago by
Michael
53k • written 2 days ago by
camillab.
▴ 130
0
votes
0
replies
120
views
scanpy problem for empty cells
scanpy
updated 2 days ago by
Ram
40k • written 2 days ago by
Andy
▴ 90
0
votes
0
replies
124
views
Current landscape of approaches to scRNA-seq with nanopore sequencers?
scRNA-seq
nanopore
single-cell
updated 2 days ago by
Ram
40k • written 2 days ago by
LauferVA
3.7k
0
votes
1
reply
160
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi
cli
updated 2 days ago by
Ram
40k • written 2 days ago by
O.rka
▴ 680
1
vote
0
replies
122
views
News:
Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
NCBI
Codeathon
2 days ago by
PeterC_NCBI
▴ 330
3
votes
4
replies
318
views
Chromosome bias on RNA-Seq differential gene expression analysis
chromosome-bias
RNA-seq
1 day ago by
blz
▴ 20
0
votes
1
reply
157
views
OMA in AWS cloud
OMA
AWS
updated 2 days ago by
Ram
40k • written 2 days ago by
Ksel
• 0
0
votes
6
replies
309
views
genome data downloads for various strains
gisaid
hass-marr
updated 2 days ago by
Ram
40k • written 2 days ago by
iftikharmaryam123
• 0
0
votes
0
replies
146
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
2 days ago by
juliviglino
• 0
3
votes
2
replies
289
views
Identifying common DEGs among multiple datasets
R
DEG
updated 2 days ago by
Barry Digby
★ 1.2k • written 3 days ago by
Shma
• 0
3
votes
5
replies
402
views
Assistance with Fungal Genome Annotation Using Maker and BLAST
gff3
fasta
maker
xml
blastp
updated 1 day ago by
Mensur Dlakic
★ 24k • written 3 days ago by
Edoardo
• 0
0
votes
0
replies
134
views
News:
Workshop - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)
workshop
scRNA-Seq
RNA-Seq
single-cell
updated 2 days ago by
Ram
40k • written 2 days ago by
David Langenberger
10k
2
votes
3
replies
316
views
Forum:
Importance of Data Structures for Bioinformatics?
data-structures
updated 2 days ago by
Ram
40k • written 3 days ago by
S
• 0
0
votes
2
replies
249
views
How to find positions with higher depth relative to their surroundings
depth
python
samtools
updated 2 days ago by
xiaoguang
▴ 120 • written 3 days ago by
hyperdx1
• 0
0
votes
0
replies
142
views
News:
Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
sequence-analysis
sars-cov-2
spike-protein
updated 2 days ago by
Ram
40k • written 2 days ago by
Prem
• 0
112,609 results • Page
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smrutimayipanda
▴ 20
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Jeremy Leipzig
21k
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alserg
▴ 860
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Recent Replies
Comment: Dotplot error: subscript out of bound
by
Xuhao
• 0
Got it. Thanks a lot.
Comment: Merging the filename with tsv files for master file
by
smrutimayipanda
▴ 20
this is the code which I have written: import os import pandas as pd # Get the list of all the orf.tsv files orf_tsv_…
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
There are plenty of variants that don't exist in gnomAD - only 759M SNPs (chr-pos-ref-alt) out of a possible 9B. Your question is a bit con…
Comment: Modify the code to take most abundant reads from a cluster and process it.
by
Mohd
▴ 40
Hi, Thanks for the help. I am just a beginner and the code was written by someone else, I am trying to modify it for myself. I will try to …
Comment: Hugo_Symbol to Entrez ID
by
GenoMax
134k
Using `EntrezDirect` ([**LINK**][1]): $ esearch -db gene -query "TSPAN6 [gene] AND human [orgn]" | esummary | xtract -pattern Document…
Comment: Ties in reranked list
by
Hamza
• 0
I had actually accidentally used ranks instead of Entrez gene ids (but switched later to human Ensembl gene ids). However, without your com…
Comment: Hugo_Symbol to Entrez ID
by
shakyaram079
• 0
Yes sure. These are all gene IDs BZRAP1, C19orf60, TCEB3 and so on.
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
• 0
I tried the commands you recommended in the bash/command line. When I tried `find "${bam_directory}" -type f -name "*.bam" | xargs samtools…
Comment: Hugo_Symbol to Entrez ID
by
GenoMax
134k
Can you provide some examples of HUGO ID's you are unable to convert?
Comment: Using STAR aligner to build index of hg38
by
GenoMax
134k
GTF file includes gene models/annotation information. You could also use a program like `salmon/kallisto` with just human transcriptome to…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Pierre Lindenbaum
157k
then test each files. find "${bam_directory}" -type f -name "*.bam" | xargs samtools quickcheck file "${reference_gen…
Answer: Ties in reranked list
by
alserg
▴ 860
The problem here is not the ties, but that your gene IDs in the pathway list (ensemble human genes) does not match the names of the stats v…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
• 0
I did not use the space between the `-u` flag and the `-o` flag (the blank line) but I did do what you recommended: # Run CuffDiff wit…
Answer: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Pierre Lindenbaum
157k
how about simply trying: ``` cuffdiff -u "${annotation_gtf}" \ -o "${output_directory}" \ -b "${reference_genome}" \ -p "${num_th…
Comment: Using STAR aligner to build index of hg38
by
Grace
• 0
Yes, I know also need a GTF file. So the GTF file will include RNA information? Thanks for your answer!!
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