Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this year
all time
today
this week
this month
this year
1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
1
vote
13
replies
911
views
Samtools indexing problem during bwa mem alignment
Alignment
bwa
samtools
9 months ago by
GlouGlou
• 0
1
vote
12
replies
3.3k
views
why different outputs with applying various extracting fasta sequences tool, which one correct!?
alignment
sequencing
RNA-Seq
updated 5 months ago by
Ram
38k • written 7.6 years ago by
seta
★ 1.8k
2
votes
12
replies
550
views
how to align an intron from a complex
genomic
updated 9 months ago by
WouterDeCoster
47k • written 9 months ago by
Bioinfo
• 0
2
votes
12
replies
1.8k
views
Nothing will align with HTSeq?
RNA-Seq
htseq
updated 6 months ago by
Ram
38k • written 7.5 years ago by
Kristin Muench
▴ 610
1
vote
12
replies
1.1k
views
Volcano plot interpretation
EnhancedVolcano
volcano-plot
updated 5 weeks ago by
Ram
38k • written 20 months ago by
fahim
▴ 20
2
votes
12
replies
4.1k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 6 weeks ago by
Ram
38k • written 7.9 years ago by
cmogren
▴ 20
0
votes
12
replies
835
views
Can't exec "cd": No such file or directory at ./PAst.pl line 43
PAst
updated 10 months ago by
lieven.sterck
14k • written 11 months ago by
Neel
▴ 10
1
vote
12
replies
3.5k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 10 weeks ago by
ATpoint
70k • written 5.5 years ago by
SMILE
▴ 170
0
votes
12
replies
2.0k
views
Tax4Fun2 - error
tax4fun
silva
blast
updated 7 months ago by
GenoMax
127k • written 13 months ago by
ymj
▴ 10
1
vote
12
replies
3.1k
views
How to run multiple alignment and SNP-calling of WGS data in .gb and .fasta using Python or Ruby/Java or any free software?
alignment
sequencing
software
updated 9 months ago by
Ram
38k • written 8.0 years ago by
fashiondesignrussian
▴ 60
0
votes
12
replies
1.5k
views
bedtools intersect issue
bed
bedtools
updated 1 day ago by
Ram
38k • written 4.6 years ago by
elisheva
▴ 120
6
votes
12
replies
1.1k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 6 days ago by
Ram
38k • written 4.2 years ago by
english.server
▴ 290
1
vote
12
replies
655
views
weird alignment results for RNAseq data
hisat2
star
updated 11 months ago by
cpad0112
21k • written 11 months ago by
Sara
▴ 220
4
votes
12
replies
900
views
Bulk RNA seq: all p adjusted are the same
p-adj
RNA-seq
differential-gene-expression
updated 3 months ago by
Ram
38k • written 10 months ago by
nils.simon.biology
▴ 10
2
votes
12
replies
1.2k
views
The best way to get gene lengths for 15K+ genes?
r
EDAseq
RNA-seq
5 months ago by
JACKY
▴ 80
6
votes
12
replies
1.2k
views
VCF files 101 - for people from non Bioinformatics Background
vcf
sequencing
genome
variant-calling
updated 9 days ago by
Ram
38k • written 2.6 years ago by
akshaykum684
▴ 20
0
votes
12
replies
3.5k
views
Problem: kmergenie has a minimum number of input of reads?
K-mers
Kmergenie
updated 10 months ago by
Ram
38k • written 8.1 years ago by
Leandro de Mattos
▴ 90
0
votes
12
replies
2.6k
views
Allpaths- Keep getting ConvertToFastbQualb.pl failed for group 'paired_ends' when I run PrepareAllPaths
next-gen
Assembly
updated 3 months ago by
Ram
38k • written 7.7 years ago by
mafireyi
▴ 80
0
votes
12
replies
896
views
Splitting CRAM files
CRAM-files
sequence-alignment
3 months ago by
langziv
▴ 20
5
votes
12
replies
522
views
Data from an experiment
single-cell
updated 5 weeks ago by
GenoMax
127k • written 5 weeks ago by
Chris
▴ 70
1
vote
12
replies
3.1k
views
dN/dS analysis of genomes
genome
sequence
alignment
5 months ago by
Mehmet
▴ 790
8
votes
12
replies
2.4k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 6 days ago by
Ram
38k • written 19 months ago by
daver.v
▴ 30
5
votes
11
replies
3.0k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 8 days ago by
Ram
38k • written 4.9 years ago by
HG
▴ 30
1
vote
11
replies
4.0k
views
Running survival analysis using Rplink
Cox
Survival
R
GWAS
PLINK
updated 12 months ago by
Ram
38k • written 8.2 years ago by
Caragh
▴ 40
4
votes
11
replies
1.0k
views
Running STAR
STAR
7 months ago by
Chris
▴ 70
0
votes
11
replies
1.2k
views
Error in Importing data in qiime2
Metagenomics
Sequencing
Qiime2
Amplicon
8 months ago by
Vaishnavi
• 0
6
votes
11
replies
704
views
Calculate RPKM
RPKM
2 days ago by
Chris
▴ 70
5
votes
11
replies
6.3k
views
Error while running miso
RNA-Seq
splicing
updated 7 months ago by
Ram
38k • written 7.6 years ago by
priyankamaripuri
▴ 40
1
vote
11
replies
2.8k
views
merge samples in phyloseq returns NAs
R
phyloseq
biom
updated 4 months ago by
joe.e.weaver
• 0 • written 2.7 years ago by
annaA
▴ 10
0
votes
11
replies
2.3k
views
mpiBLAST Score and E-value Calculation
blast
sequence
updated 9 months ago by
Ram
38k • written 8.0 years ago by
Lakshman Rao
• 0
4
votes
11
replies
2.3k
views
7 follow
Getting coding sequence length
NCBI
Gene
CDS
updated 9 months ago by
newbio17
▴ 350 • written 2.7 years ago by
fi1d18
★ 4.1k
3
votes
11
replies
784
views
RepeatMasker error
repeatmasking
transciptome
RNA-seq
updated 8 months ago by
mark.ziemann
★ 1.8k • written 8 months ago by
barrypraveen
▴ 100
4
votes
11
replies
2.6k
views
Please add an explicit type tag :NAME
software-error
next-gen
genome
updated 7 weeks ago by
Ram
38k • written 4.9 years ago by
mahdikhadem95
▴ 30
8
votes
11
replies
1.2k
views
using STAR instead of HISAT2
STAR
updated 7 months ago by
Ram
38k • written 8 months ago by
Chris
▴ 70
3
votes
11
replies
12k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq
RNA-Seq
STAR
updated 11 months ago by
Ram
38k • written 8.2 years ago by
noushin.farnoud
▴ 120
0
votes
11
replies
751
views
Problem with Trimmomatic Multiple Paired-End sequencing.
Trimmomatic
updated 9 weeks ago by
GenoMax
127k • written 9 weeks ago by
john
• 0
10
votes
11
replies
8.2k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 9 months ago by
Ram
38k • written 8.0 years ago by
SheelS
▴ 40
0
votes
11
replies
797
views
Python - Samtools mpileup find snps with allele frequency
snp
mpileup
python
samtools
8 months ago by
pablosolar.r
▴ 20
4
votes
11
replies
5.6k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
7 months ago by
prasundutta87
▴ 650
1
vote
11
replies
2.9k
views
bedtools fisher interpretation of "in -a" "not in -b"
fisher
bedtools
intersection
updated 5 weeks ago by
Ram
38k • written 5.1 years ago by
jomo018
▴ 690
3
votes
11
replies
995
views
Feature count is very low using htseq-count
htseq
bbmap
11 months ago by
salmon
▴ 10
3
votes
10
replies
3.1k
views
Somaticsniper Hangs Up
updated 11 months ago by
Ram
38k • written 9.1 years ago by
Jack
▴ 80
0
votes
10
replies
747
views
using txt file to pass pathways for pipelines
muscle
seqkit
bash
fasta
updated 8 months ago by
Ram
38k • written 8 months ago by
Hugo
• 0
2
votes
10
replies
5.9k
views
fq.gz file use
BioEdit
R
updated 5 days ago by
Ram
38k • written 4.1 years ago by
choi.yisoo.hi
• 0
5
votes
10
replies
4.5k
views
Antisense transcription - how to detect it?
RNA-Seq
antisense
updated 6 months ago by
Ram
38k • written 7.4 years ago by
John
13k
2
votes
10
replies
684
views
R-studio freezes error
RStudio
offtopic
updated 5 months ago by
Ram
38k • written 5 months ago by
Amr
▴ 140
0
votes
10
replies
969
views
DeSeq2 "some values in assay are negative"
RNAseq
4 months ago by
Morris_Chair
▴ 330
3
votes
10
replies
981
views
how to delete a file 3 months after downloading it in python
python
pandas
updated 10 months ago by
ATpoint
70k • written 21 months ago by
Debut
▴ 20
3
votes
10
replies
736
views
Error with FindConservedMarkers()
FindConservedMarkers
5 weeks ago by
Chris
▴ 70
4
votes
10
replies
357
views
Extract unmapped reads OR reads covering chromosome 6 from a bam file?
fastq
bam
samtools
picard
5 weeks ago by
dps2501
▴ 20
1,000 results • Page
2 of 20
Recent Votes
Answer: PCA in gene expression
Answer: PCA in gene expression
Comment: Enrichment analysis based on kegg for zebrafish
Question on number of possible alignments
Comment: ExomeDepth installation error
Answer: ExomeDepth installation error
Comment: Run nextflow sections sequentially
Recent Locations •
All
United States,
1 minute ago
Netherlands,
2 minutes ago
United States,
2 minutes ago
United States,
3 minutes ago
United Kingdom,
4 minutes ago
Israel,
4 minutes ago
University Park, USA,
5 minutes ago
Recent Awards •
All
Guru
to
jv
★ 1.0k
Popular Question
to
Kumar
▴ 150
Popular Question
to
rebeliscu
▴ 50
Commentator
to
Pierre Lindenbaum
153k
Scholar
to
100dustedclays
▴ 10
Popular Question
to
abdelmalek.benmeziane
• 0
Teacher
to
MirianT_NCBI
▴ 440
Recent Replies
Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
well, because this is not you guys' private forum, there are other people participating (not native french speaking) , just to give a reaso…
Answer: How to get gene from PSIBLAST resuts
by
lieven.sterck
14k
what you likely will need to do: 1. get the ID of the protein that you are interested in (out of result from PSIBLAST) 2. lookup that…
Answer: How to analize multiple letters codes in COG IDs?
by
Mensur Dlakic
★ 23k
The meaning of individual letters is described in a well-known COG functional code: https://ecoliwiki.org/colipedia/index.php/Clusters_o…
Comment: How to find promoter sequence of a gene?
by
sunyeping
▴ 40
The organism is mice.
Answer: How to generate GFF/GTF file from cDNA transcipts FASTA file?
by
Pierre Lindenbaum
153k
BLAT your cDNAs to the reference. This should be a PSL file that can be converted to a psl->gff3 converter (e.g: https://github.com/gperte…
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs?
by
Darked89
4.2k
You may try to check what happened with DEGs obtained using the 300 fragments assembly by getting the sequences of these genes and comparin…
Comment: ExomeDepth installation error
by
Medha
• 0
Thanks, that did work. Also in next steps, there are some arguments like bam.files, I was wondering do we require to have multiple bam fil…
Comment: ExomeDepth installation error
by
jared.andrews07
★ 14k
No idea, I don't use databricks. I'd read the docs, find a local expert to help you out, or contact their support, likely in that order.
Comment: ExomeDepth installation error
by
Medha
• 0
Hi @jaredandrews07 thanks for reverting back. I am new to R and just want to make sure ExomeDepth is working for the first time. For the Rs…
Comment: Embedded stop codon in translated nucleotide sequences in DAMBE
by
Mensur Dlakic
★ 23k
It is not obvious to me what exact steps you did here, but here is what I do know: there will always be stop codons even in open reading fr…
Comment: Error with a function in ATAC-seq analysis
by
Chris
▴ 70
So you skip the GRanges()? Yes, no error anymore but I am not sure if that causes changing in downstream analysis.
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
by
jv
★ 1.0k
`stringr::str_remove` can remove " - Mus musculus (house mouse)" from the pathway names which are stored under `KEGGPATHID2NAME$to` in your…
Comment: Error with a function in ATAC-seq analysis
by
jv
★ 1.0k
run `union` on the data frames
Comment: PCA in gene expression
by
ali
• 0
Thanks for your attention. yes I know that we should not omit the samples, I just worry about noises on my differential expression and some…
Comment: Error with a function in ATAC-seq analysis
by
Chris
▴ 70
Yes, it is not a vector. Formal class 'GRanges' Because GRanges() function made it become a Granges class which is a data frame before tha…
Traffic: 2897 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6