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1,000 results • Page
5 of 20
Sort: replies
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Views
Votes
Replies
0
votes
15
replies
3.3k
views
bcftools multiple samples
snp
4.5 years ago by
evelyn
▴ 230
1
vote
15
replies
3.7k
views
Fastx quality filter
next-gen
RNA-Seq
software error
sequencing
updated 7.4 years ago by
Ram
43k • written 7.4 years ago by
kriti.awasthi23
▴ 10
10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
7.5 years ago by
Farbod
★ 3.4k
0
votes
15
replies
3.7k
views
Identify genes in a tophat aligned bam/sam file
blast
alignment
rna-seq
gene
updated 16 months ago by
Ram
43k • written 8.9 years ago by
gchaves
• 0
6
votes
15
replies
1.6k
views
The Best Cloud Solution For Genomics
cloud
data-sharing
genomics
workflow
updated 22 months ago by
Ram
43k • written 23 months ago by
davidmaimoun
▴ 50
3
votes
15
replies
2.8k
views
fastq reads with primers and truseq indexed adapter
sequencing
next-gen
sequence
7.2 years ago by
jomo018
▴ 720
7
votes
15
replies
2.1k
views
cufflinks in loop
rna-seq
RNA-Seq
genome
updated 5.9 years ago by
finswimmer
16k • written 5.9 years ago by
suny.bio
• 0
1
vote
15
replies
4.4k
views
Ultrafast alignment of short sequences to a genome (with up to 5 mismatches!)
genome
alignment
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
Aurelie MLB
▴ 360
3
votes
15
replies
2.1k
views
Overlapping regions in a BED file
regions
BED
Sequence
exons
annotation
22 months ago by
Matej
• 0
7
votes
15
replies
7.2k
views
6 follow
blastn error - NCBI C++ Exception
assembly
blast
alignment
updated 2.1 years ago by
lieven.sterck
15k • written 3.1 years ago by
sunnykevin97
▴ 980
6
votes
15
replies
1.6k
views
Reads partly within an exon
RNA-Seq
6.8 years ago by
benjyrolls
▴ 70
6
votes
15
replies
8.5k
views
Strand specific protocol for bowtie2 alignment
bowtie2
rnaseq
alignment
RNA-Seq
updated 2.5 years ago by
Ram
43k • written 8.5 years ago by
nalandaatmi
▴ 100
8
votes
15
replies
2.0k
views
RNAseq differential expression analysis : no significative FDR but significative GO enrichment
RNA-Seq
differential expression
4.6 years ago by
guillaume.rbt
★ 1.0k
2
votes
15
replies
4.2k
views
How to interpret reads mapped to genome from samtools flagstat vs TopHat align_summary.txt ?
RNA-Seq
8.1 years ago by
Vasu
▴ 770
1
vote
15
replies
3.4k
views
How to perform multiple alignment using MAFFT?
genome
alignment
gene
sequence
3.1 years ago by
anikcropscience
▴ 230
2
votes
15
replies
2.2k
views
to get each covariate with PC loading in PCA
RNA-seq
PCA
5.3 years ago by
Grace_G
▴ 20
2
votes
15
replies
4.1k
views
Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
next-gen
SNP
alignment
updated 4.1 years ago by
wm
▴ 560 • written 4.1 years ago by
shrutidabral
▴ 10
4
votes
15
replies
4.0k
views
Paired-read alignment length from BAM/SAM file
bam
sam
paired-read
alignment
6.9 years ago by
Soumitra Pal
▴ 10
5
votes
15
replies
1.6k
views
NGS Sequencing depths
next-gen
sequencing
gene
7.2 years ago by
sliproach
▴ 10
3
votes
15
replies
3.2k
views
Less and less genes predicted with each iteration of SNAP/MAKER
maker
annotation
snap
gene prediction
genomics
updated 2.7 years ago by
jaredbernard
▴ 30 • written 4.1 years ago by
mrmrwinter
▴ 30
1
vote
15
replies
2.0k
views
Samtools merge Illumina and PB bam file empty
Illumina
samtools
Bam
PacBio
updated 14 months ago by
Ram
43k • written 3.8 years ago by
talbots
▴ 30
0
votes
15
replies
3.2k
views
SAMFormatException: Did not inflate expected amount error
WES
updated 2.5 years ago by
greekkey
▴ 20 • written 2.9 years ago by
smrutimayipanda
▴ 20
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
5 months ago by
analyst
▴ 50
6
votes
15
replies
2.7k
views
Why can't I reproduce the same heat map
ggplots
R
RNA-Seq
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
Za
▴ 140
0
votes
15
replies
2.6k
views
Strategy for generating a consensus sequence for 100 complete bacterial genomes?
consensus seq
mauve
5.9 years ago by
Alec Watanabe
▴ 60
10
votes
15
replies
6.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 14 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
20
votes
15
replies
30k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 21 months ago by
Ram
43k • written 8.4 years ago by
dam4l
▴ 200
7
votes
15
replies
4.3k
views
Biopython Pairwise Alignment output
biopython
needleman
global alignment
4.1 years ago by
tommaso.green
• 0
3
votes
15
replies
2.4k
views
RNA Seq Analysis:Feature Counts are zero
RNA-Seq
feature counts
updated 3.9 years ago by
Biostar
20 • written 3.9 years ago by
Genomics
▴ 20
4
votes
15
replies
3.3k
views
Adding Multiple readgroups to BAM file
GATK
ReadGroups
8.1 years ago by
vakul.mohanty
▴ 270
2
votes
15
replies
1.6k
views
from protein to tRNA combinations
RNA-Seq
rna-seq
written 3.4 years ago by
shiningsky000
• 0
5
votes
15
replies
2.1k
views
Sample contamination level over 30%
next-gen
6.6 years ago by
haiying.kong
▴ 360
1
vote
15
replies
3.7k
views
Install Lefse in Ubuntu 12
install
lefse
microbiome
5.9 years ago by
goh
▴ 10
2
votes
14
replies
1.1k
views
heatmap for HTSeq data in R
RNA-Seq
updated 3.5 years ago by
Ram
43k • written 3.5 years ago by
Rob
▴ 170
1
vote
14
replies
3.8k
views
Picard MarkDuplicates shows error (removing pcr duplicates)
snp
alignment
sequence
updated 5.5 years ago by
Kevin Blighe
88k • written 5.5 years ago by
ashaneev07
▴ 20
4
votes
14
replies
3.6k
views
6 follow
Cutadapt installation - user defined directory
cutadapt Installation
5.8 years ago by
davide.chiarugi
▴ 20
15
votes
14
replies
3.2k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
6.3 years ago by
John
▴ 270
0
votes
14
replies
3.7k
views
ABySS - Out of memory using 64 cores (520GB)
abyss
assembly
updated 19 months ago by
Ram
43k • written 8.8 years ago by
wjar6718
• 0
1
vote
14
replies
2.8k
views
Comparing two variant files
variant
comparison
updated 3.0 years ago by
prasundutta87
▴ 660 • written 3.0 years ago by
shivangi.agarwal800
▴ 120
8
votes
14
replies
2.4k
views
6 follow
Definition of "=" in comparing two genes
sequencing
gene
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
rdorey
• 0
0
votes
14
replies
768
views
frma normalization
affybatch
frma
mcp-counter
12 weeks ago by
michelafrancesconi9
▴ 20
5
votes
14
replies
1.6k
views
Alzheimer's disease and its classification
SNP
R
machine learning
5.5 years ago by
bioinfo456
▴ 150
3
votes
14
replies
6.0k
views
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
blastn
mbedtls
blast
linux
blast+
updated 3 months ago by
K.Gee
▴ 40 • written 3.1 years ago by
janneken0210
• 0
12
votes
14
replies
5.8k
views
bedtools intersect error?
ChIP-Seq
bedtools
intersect
5.2 years ago by
star
▴ 350
0
votes
14
replies
3.2k
views
DESeq2 output and GO analysis
RNA-Seq
GO
4.9 years ago by
2nelly
▴ 310
0
votes
14
replies
3.0k
views
NCBI Genome Remapping Service- clinical remap
SNP
co-ordinate remapping
updated 5.9 years ago by
Ram
43k • written 5.9 years ago by
Sudhir Jadhao
▴ 70
0
votes
14
replies
3.0k
views
Creating coverage files containing paired-end fragments of particular sizes
BAM
bigwig
wig
bed
paired-end
7.1 years ago by
mmmmcandrew
▴ 190
1
vote
14
replies
3.1k
views
In this Python script I want to save result of print(traj_rmsd) in an output.xvg file. I am unable to open this file and it's showing following mess…
mdtraj
python
molecular dyanamics
updated 7.3 years ago by
Ram
43k • written 7.3 years ago by
naveen100787
• 0
7
votes
14
replies
5.0k
views
How to Calulate Allele Frequency from a VCF File?
frequency
allele
VCF
updated 15 months ago by
Jeremy Leipzig
22k • written 15 months ago by
Emoji
▴ 10
7
votes
14
replies
2.1k
views
single-cell exome sequencing pipeline
SNP
exom
single-cell
next-gen
7.6 years ago by
zizigolu
★ 4.3k
1,000 results • Page
5 of 20
Recent Votes
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
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Recent Replies
Comment: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
by
Ash
• 0
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
Comment: Doubt about the process of annotation, detection, identification and classificat
by
MarcosCosta
• 0
Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
• 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
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