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 : all time
all time
today
this week
this month
this year
1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
1
vote
13
replies
12k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 2.3 years ago by
darklings
▴ 520 • written 4.0 years ago by
gordo2b
• 0
0
votes
1
reply
12k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 7.2 years ago by
Biostar
20 • written 7.2 years ago by
rednalf
▴ 90
0
votes
3
replies
12k
views
edgeR: likelihood ratio test or quasi-likelihood F-test?
R
rna-seq
next-gen
6.5 years ago by
moxu
▴ 510
2
votes
13
replies
12k
views
8 follow
(ERR): bowtie2-align exited with value 1
software error
RNA-Seq
updated 5.7 years ago by
basucsmcri
• 0 • written 6.6 years ago by
biostarsb
▴ 30
3
votes
2
replies
12k
views
ExAC PLI score calculation
DNA-Seq
6.6 years ago by
jonessara770
▴ 240
4
votes
9
replies
12k
views
Seqtk subseq: structure of file name.lst
sequence
next-gen
updated 5.4 years ago by
Ram
40k • written 5.4 years ago by
ste.lu
▴ 80
0
votes
3
replies
11k
views
Extracting Specific Columns from Multiple Files & Writing to File Python
python
file-handeling
7.4 years ago by
BioICoder
▴ 40
7
votes
9
replies
11k
views
Different alignment rates for Hisat2 and STAR, Hisat2 has lower alignment rate and STAR have many multi aligned reads
RNA-Seq
updated 6.0 years ago by
Satyajeet Khare
★ 1.6k • written 6.0 years ago by
SMILE
▴ 170
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 10 months ago by
Ram
40k • written 8.2 years ago by
biolab
★ 1.4k
1
vote
13
replies
11k
views
MarkDuplicates memory issue
alignment
Picard
MarkDuplicates
7.7 years ago by
cacampbell
▴ 50
0
votes
4
replies
11k
views
Convert .gbf file to .gbk or .gff
gbk
gff
gbf
updated 8 months ago by
Ram
40k • written 8.4 years ago by
che.bellaj
• 0
3
votes
8
replies
11k
views
6 follow
How do I go from UniProt ID to retrieving the gene name?
sequence
5.9 years ago by
a.rex
▴ 350
4
votes
7
replies
11k
views
Grab Coordinate Of Centromeres From Ucsc
ucsc
10.4 years ago by
jeansimon32
▴ 170
2
votes
3
replies
11k
views
converting maf to vcf
Exome
maf2vcf
updated 8 months ago by
Ram
40k • written 8.4 years ago by
ashishchahl
• 0
3
votes
4
replies
11k
views
Zlib.Error: -3 While Decompressing: Invalid Distance To Far Back (By Using Macs For Chip-Seq Data)
error
12.0 years ago by
Lisanne
• 0
13
votes
6
replies
11k
views
6 follow
MAF vs VAF
sequencing
5.5 years ago by
lauren.wahyudi
▴ 40
41
votes
55
replies
11k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.5 years ago by
midox
▴ 290
1
vote
2
replies
11k
views
Downloading BAM files GEO/SRA
bam
sra
geo
samtools
sratoolkit
7.2 years ago by
ilobelo
▴ 10
6
votes
7
replies
11k
views
bedtools intersect bed and vcf, coordinates problem
bedtools
bed
vcf
6.5 years ago by
abascalfederico
★ 1.2k
2
votes
4
replies
11k
views
Pymol-Generate Pymol Movie To Mpeg
pymol
updated 20 months ago by
Ram
40k • written 11.7 years ago by
Reyhaneh
▴ 530
3
votes
16
replies
11k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 3 months ago by
Ram
40k • written 4.5 years ago by
Star
▴ 60
2
votes
8
replies
11k
views
Loading Custom Genome In Igv Is Not Displaying Genes, Names Match.
igv
gff
reference
contigs
11.6 years ago by
Nickengland
▴ 130
4
votes
14
replies
10k
views
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
mapping quality
STAR
BWA
alignment
7.2 years ago by
kirannbishwa01
★ 1.6k
3
votes
4
replies
10k
views
basename: missing operand
snp
4.2 years ago by
evelyn
▴ 220
2
votes
0
replies
10k
views
How to plot UniFrac PCoA with 95% confidence Elipses in R
metagenomics
ordiellipse
vegan
R
phyloseq
updated 18 months ago by
Ram
40k • written 8.7 years ago by
c.v.oflynn
▴ 100
3
votes
1
reply
10k
views
Negative P-Values
gene
genome
next-gen-sequencing
updated 13 months ago by
Ram
40k • written 8.1 years ago by
stevenlang123
▴ 200
7
votes
8
replies
10k
views
Picard tools duplicate removal
RNA-Seq
picard-tools
5.9 years ago by
blur
▴ 280
2
votes
1
reply
10k
views
Calculate Linkage Disequilibrium For Snps (Using R^2)
snp
linkage
10.2 years ago by
TitoPullo
▴ 180
3
votes
2
replies
10k
views
BWA-MEM Vs BWA-ALN
next-gen
genome
alignment
7.4 years ago by
SOHAIL
▴ 400
0
votes
1
reply
10k
views
Is it normal that nearly all of p-value is equal to 0.1 in PERMANOVA analysis
PERMANOVA
statistics
metagenomics
updated 2.8 years ago by
dqq102829
• 0 • written 3.7 years ago by
zhangdengwei
▴ 210
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 21 months ago by
Ram
40k • written 9.1 years ago by
trakhtenberg
▴ 160
1
vote
2
replies
10.0k
views
Converting MSTRG from stringtie with gene name
RNA-Seq
Stringtie
updated 5.7 years ago by
Biostar
20 • written 5.7 years ago by
fhassanz
▴ 20
3
votes
9
replies
10.0k
views
Error with samtools faidx...Different line length in sequence
samtools
faidx
updated 5.3 years ago by
Biostar
20 • written 5.5 years ago by
oars
▴ 190
0
votes
0
replies
10.0k
views
Map Between Uniprot Accesion And Gene.Symbol Using R Or/And Mysql
r
bioconductor
mysql
9.7 years ago by
jfertaj
▴ 110
2
votes
2
replies
9.9k
views
How to make clusters in heat map using ggplot2?
RNA-Seq
rna-seq
R
4.4 years ago by
John
▴ 270
1
vote
1
reply
9.9k
views
Raxml bootstrap support values
figtree
raxml
bootstrap
updated 24 months ago by
Ram
40k • written 9.4 years ago by
JackBel
• 0
3
votes
6
replies
9.9k
views
6 follow
How to calculate genetic correlation with R
R
updated 16 months ago by
ibomsolomon
• 0 • written 9.4 years ago by
Tohamy
▴ 80
7
votes
9
replies
9.8k
views
Samtools Index Segmentation Fault
samtools
index
9.5 years ago by
Noushin N
▴ 600
0
votes
0
replies
9.8k
views
pheatmap row annotation and title font size questions
heatmap
pheatmap
updated 8 months ago by
Ram
40k • written 8.3 years ago by
neokao
• 0
1
vote
5
replies
9.8k
views
What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With Gatk?
bed
agilent
gatk
updated 3.6 years ago by
Karma
▴ 310 • written 9.8 years ago by
newDNASeqer
▴ 750
2
votes
16
replies
9.7k
views
Tophat with Bowtie2 long index
tophat
bowtie
updated 20 months ago by
Ram
40k • written 9.2 years ago by
BDK_compbio
▴ 140
13
votes
22
replies
9.7k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 6.0 years ago by
Biostar
20 • written 6.2 years ago by
lessismore
★ 1.3k
2
votes
8
replies
9.6k
views
Size of typical genomic data
genomic
updated 6 months ago by
Ram
40k • written 5.4 years ago by
Nicolas Rosewick
10k
3
votes
10
replies
9.5k
views
How can I obtain SNP from TCGA?
Risky-allele
BRCA
SNP
updated 20 months ago by
Ram
40k • written 9.0 years ago by
purmod
▴ 10
3
votes
3
replies
9.4k
views
bcftools mpileup output format
bcftools
mpileup
5.1 years ago by
tarek.mohamed
▴ 350
3
votes
4
replies
9.4k
views
Aligning RNA seq data to genome or transcriptome
RNA-Seq
ngs
transcriptome
genome
updated 6.0 years ago by
Ram
40k • written 6.0 years ago by
KVC_bioinfo
▴ 590
0
votes
2
replies
9.4k
views
DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' must not be length 0
RNA-Seq
DESeq2
gpar
pheatmap
5.9 years ago by
Anthony.Knox
▴ 60
6
votes
3
replies
9.4k
views
Sequence duplication levels-RNA Seq
RNA-Seq
updated 3.0 years ago by
joshua.theisen
▴ 30 • written 5.5 years ago by
makwana.kd
▴ 50
0
votes
8
replies
9.4k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 3 months ago by
Ram
40k • written 6.2 years ago by
himanimalhotra89
• 0
5
votes
8
replies
9.3k
views
7 follow
Converting SNP names from Illumina GSA array to rsID using PLINK
SNP
plink
6.0 years ago by
dam4l
▴ 190
1,000 results • Page
2 of 20
Recent Votes
Concatenating fastq.gz files across lanes
A: Concatenating fastq.gz files across lanes
Answer: bedGraph for Coverage of Insert from Paired-End Data?
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
Human Genomics Team Leader
Recent Locations •
All
Bangladesh,
just now
Germany,
1 minute ago
India,
1 minute ago
University Park, USA,
2 minutes ago
Glasgow, UK,
3 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
4 minutes ago
Bologna,
4 minutes ago
Recent Awards •
All
Popular Question
to
adeizadavid
▴ 10
Popular Question
to
dec986
▴ 370
Popular Question
to
arriyaz.nstu
▴ 30
Popular Question
to
gyspace
• 0
Teacher
to
ATpoint
76k
Popular Question
to
amy__
▴ 150
Popular Question
to
David Langenberger
10k
Recent Replies
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴ 10
yes @juke34 , I tried agat_sp_compare_two_annotations.pl for both gff files and got comparative output in table format. Thank you very muc…
Comment: Integrated Seurat object change name of the two conditions
by
Amitm
★ 2.2k
Yes, its similar structure. This snippet should add a new metadata column "sample.New" with what you want to do # Assuming a seurat obj. c…
Comment: Low Alignment rate
by
biofalconch
▴ 960
Yeap, you can sample your reads with `seqtk` like this: seqtk sample -s100 read2.fq 100 > Sample.fq Take a couple and run them throug…
Answer: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★ 1.2k
You won't find them on circBase. circAtlas has the mature spliced sequence available. You can [search for circRNAs](https://ngdc.cncb.a…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
Ram
40k
\#TIL mambaforge - better than continuum's conda images I'm guessing?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
arriyaz.nstu
▴ 30
If the laptop doesn't support WSL2, then will the Docker (with linux) work?
Comment: Integrated Seurat object change name of the two conditions
by
camillab.
▴ 130
thanks but my metadata looks different from yours. Will it work even there are not the same "structure"? or…
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
Docker is great, I use it daily since you're independent of the host computer and can share and pull the images via DockerHub. It's also gr…
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact?
by
ATpoint
76k
If you do DE analysis on single-cell level then I find it critical to enforce some cutoff, as many cells means a lot of power so you get ev…
Comment: Visualize where kmers are on a reference genome
by
Ram
40k
Did you google "visualize BED file on genome"?<a href="" title="Text added because biostars parser needs it"></a>
Comment: obtaining circular RNAs' sequences from circBase
by
Ram
40k
> as you know No I did not. I know this is a cultural mannerism but it's antiquated. Please abandon this phrase, it can come across as con…
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact?
by
omer.shomrat
• 0
Thanks a lot for the response! I'm doing pathway enrichment analysis (using clusterProfiler) on almost all genes in each cluster, with the…
Comment: Unable to build applet in DNAnexus, .jar file not found
by
Ram
40k
Ah I missed the part where DNANexus makes this problem out of our reach. Thank you, GenoMax!
Answer: Unable to build applet in DNAnexus, .jar file not found
by
Ram
40k
That's not how `$PATH` works. Place your jar file in any accessible location, then add a script to your `/usr/local/bin` like so: ``` #…
Comment: Unable to build applet in DNAnexus, .jar file not found
by
GenoMax
134k
Please contact DNANexus support. That may be your best bet since this is commercial software and not many here will have access.
Traffic: 4355 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