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314 results • Page
1 of 7
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Votes
Replies
10
votes
6
replies
2.5k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 22 minutes ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
8
votes
12
replies
2.4k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 4 days ago by
Ram
38k • written 19 months ago by
daver.v
▴ 30
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 5 hours ago by
Ram
38k • written 22 months ago by
Debut
▴ 20
7
votes
10
replies
1.1k
views
col as names [solved]
R
updated 4 days ago by
Ram
38k • written 4.0 years ago by
demoraesdiogo2017
▴ 90
7
votes
4
replies
1.7k
views
useful and freely available softwares for Bioinformatics
software
updated 4 days ago by
Ram
38k • written 8.0 years ago by
Mo
▴ 920
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 22 hours ago by
Ram
38k • written 7.9 years ago by
gaurav.singh
▴ 10
6
votes
11
replies
676
views
Calculate RPKM
RPKM
15 hours ago by
Chris
▴ 70
6
votes
12
replies
1.1k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 4 days ago by
Ram
38k • written 4.2 years ago by
english.server
▴ 290
5
votes
11
replies
3.0k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 6 days ago by
Ram
38k • written 4.9 years ago by
HG
▴ 30
3
votes
4
replies
472
views
Changing Temporary File Location for Local BLASTP to nr Database
protein
blast
nr
updated 1 day ago by
Ram
38k • written 9 weeks ago by
katieostrouchov
▴ 20
3
votes
6
replies
1.7k
views
Methods and type datastructures use by Splign?
data-structure
splign
updated 4 hours ago by
Ram
38k • written 6.4 years ago by
Esaie
▴ 160
3
votes
4
replies
3.3k
views
Mauve File Format
ncbi
gb
mauve
gbk
updated 3 days ago by
Ram
38k • written 5.4 years ago by
trionanibrannacht
• 0
3
votes
4
replies
460
views
Genome Reference Consortium Human Build - Transcriptome Size Query
GRC
updated 4 days ago by
Ram
38k • written 10 months ago by
Oligo96
• 0
2
votes
4
replies
470
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
1 day ago by
e.r.zakiev
▴ 30
2
votes
0
replies
1.5k
views
Any relation between pan genome and genome plasticity?
genome
gene
sequence
updated 5 days ago by
Ram
38k • written 8.1 years ago by
Loub
▴ 20
2
votes
2
replies
3.3k
views
dyld : Library not loaded: Reason: image not found
python
dyld
R
updated 4 days ago by
Ram
38k • written 21 months ago by
jjp55
▴ 20
2
votes
2
replies
283
views
HaplotypeCaller GENOTYPE GIVEN ALLELES doesn't genotype given alleles
Gatk
HaplotypeCaller
VCF
4 days ago by
kamanovae
▴ 80
2
votes
2
replies
687
views
Adjusting data for covariates
R
updated 4 days ago by
Ram
38k • written 2.1 years ago by
chutt
▴ 20
2
votes
3
replies
2.5k
views
Need help teasing out insertions and deletions with bcftools stats file.vcf > file.stats
bcftools
indel
vcf
insertion
deletion
updated 4 days ago by
Ram
38k • written 5.0 years ago by
oars
▴ 190
2
votes
5
replies
172
views
GATK GenotypeGVCFs explain
calling
gatk
variant
GenotypeGVCFs
updated 9 hours ago by
Pierre Lindenbaum
153k • written 11 hours ago by
Sarah
▴ 30
2
votes
3
replies
251
views
mRNA Seq
NGS
updated 4 days ago by
Ram
38k • written 6 days ago by
Yaseen
▴ 10
2
votes
10
replies
5.9k
views
fq.gz file use
BioEdit
R
updated 3 days ago by
Ram
38k • written 4.0 years ago by
choi.yisoo.hi
• 0
2
votes
1
reply
594
views
Bioinformatics exercise on extracting FASTA sequences corresponding to taxon from a microbiome sequencing experimet in another file (.TSV)
fasta
homework
updated 4 days ago by
Ram
38k • written 2.2 years ago by
flisosergio
• 0
2
votes
2
replies
54
views
Power analysis for patient samples
RNA-seq
2 hours ago by
aropri
▴ 120
2
votes
8
replies
465
views
Depth of Coverage in Mitochondrial Genome with Samtools
samtools
depth-of-coverage
Mitochondrial-genome
2 days ago by
Lida
• 0
2
votes
4
replies
582
views
Noob question: I want to use TCGA data to compare survival with mutations, how should I do it?
cancer
mutations
tcga
updated 4 days ago by
Ram
38k • written 9 months ago by
cdeantoneo31
▴ 10
2
votes
2
replies
295
views
bcftools annotate -a
bcftools
VCF
updated 4 days ago by
Ram
38k • written 19 days ago by
anasjamshed
▴ 120
2
votes
1
reply
1.4k
views
Example data to verify of RNA-Seq Analysis pipeline
hisat2
RNA-Seq
pipeline
updated 6 days ago by
Ram
38k • written 5.1 years ago by
hkarakurt
▴ 150
2
votes
2
replies
1.1k
views
How to obtain lineage information from taxid?
euitls
taxid2lineage
accession2taxid
updated 3 days ago by
Ram
38k • written 2.4 years ago by
6schulte
▴ 30
2
votes
1
reply
406
views
Bioinformatics application on data
WES
updated 4 days ago by
Ram
38k • written 19 months ago by
Sania
• 0
2
votes
10
replies
1.2k
views
multiple FASTA sequnces in to one full sequnce according to their chromosome number
NGS
FASTA
bam
updated 4 days ago by
Ram
38k • written 4.0 years ago by
Anu
• 0
2
votes
4
replies
431
views
Trouble with transcripts_id when using how_are_we_stranded_here python package
bash
sequencing
RNA-seq
4 days ago by
ashleymb1116
• 0
1
vote
1
reply
426
views
For loop to generate mean for each measurement by sex
R
updated 5 hours ago by
Ram
38k • written 2.3 years ago by
selplat21
▴ 20
1
vote
1
reply
174
views
Problem in generating the BAM files using STAR
BAM
STAR
updated 1 day ago by
Ram
38k • written 6 months ago by
boomathi.91
• 0
1
vote
3
replies
3.7k
views
How to sort fastq.gz files efficiently
fastq
sort
updated 4 days ago by
Ram
38k • written 7.0 years ago by
komal.rathi
★ 4.1k
1
vote
1
reply
477
views
How do I resemble measurements in an experimental system when simulating in r programming?
simulation
R
updated 4 hours ago by
Ram
38k • written 2.3 years ago by
bioinfonewbie
• 0
1
vote
2
replies
366
views
What's the reason and how to fix - Regression model summary - variable name is combined with a category character in R
interpretation
Model
GLM
Regression
Summary
LM
5 days ago by
ohtang7
▴ 30
1
vote
5
replies
203
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 1 hour ago by
Trivas
▴ 630 • written 9 hours ago by
TJay
• 0
1
vote
3
replies
234
views
How to extract/find the actual names of the gene_IDs if they are not fully presented in gtf.file, and link them to the Count.matrix
featureCounts
gtf
RNA-Seq
updated 22 hours ago by
GenoMax
126k • written 1 day ago by
Pegasus
▴ 80
1
vote
3
replies
347
views
DESeq2 code to perform DEG analysis
SEseq2
DEG
updated 4 days ago by
Ram
38k • written 22 days ago by
rupali
• 0
1
vote
2
replies
225
views
How much reads per cell for fusion detection with Nanopore ?
single-cell
fusion
nanopore
5 days ago by
Evan
▴ 170
1
vote
7
replies
1.2k
views
miRDeep2.pl cannot recognize reference fasta file
mirdeep2
fasta
mirna
mirdeep2.pl
mirna-sequencing
updated 4 days ago by
Ram
38k • written 3.0 years ago by
realnewbie
▴ 30
1
vote
2
replies
421
views
Where Can I Find Free Online Software That Recognizes MIMAT... MI... Accession Numbers For My MicroRNA DEG Experiment
microarray
accession-number
MicroRNA
updated 4 days ago by
Ram
38k • written 3 months ago by
Cee
• 0
1
vote
9
replies
2.6k
views
bam to fasta error using samtools
fasta
bam
updated 4 days ago by
Ram
38k • written 6.0 years ago by
christacaggiano
▴ 60
1
vote
2
replies
937
views
How to convert multiple .vcf files into single .ped (PLINK compatible files)?
vcf
ped
PLINK
WGS
updated 4 days ago by
Ram
38k • written 17 months ago by
isml2688
• 0
1
vote
0
replies
148
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
4 days ago by
Hyper_Odin
▴ 280
1
vote
1
reply
204
views
What's the correct way to map to hg38 with alternative contigs?
NGS
bwa
updated 4 days ago by
ATpoint
70k • written 4 days ago by
Belanov
▴ 10
1
vote
4
replies
759
views
Method to classify given sample into subtype
Breast-Cancer
RNA-Seq
TCGA-BRCA
TCGA
updated 4 days ago by
Ram
38k • written 2.4 years ago by
im
• 0
1
vote
1
reply
330
views
scRNA seq with seurat: how do I add a column to the metadata?
scRNA-seq
scRNA
updated 4 days ago by
Ram
38k • written 3 months ago by
cdeantoneo31
▴ 10
1
vote
3
replies
436
views
Hisat2 Script Help
hisat2
mapping
updated 4 days ago by
Ram
38k • written 8 months ago by
smithkthedale
▴ 10
314 results • Page
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Answer: wrong quality plots in fastqc output
Comment: Plot heatmap using row_splitting but splitting should based on a column in data
Comment: Power analysis for patient samples
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Answer: Problem generating a .vcf after upgrade of samtools and bcftools
by
GenoMax
126k
> I can't find the way using the man documentation of bcftools to get a > .vcf from a sorted .bam file. This should be all you need: https…
Comment: RNA-SEQ
by
Trivas
▴ 630
You should be able to do `fasterq-dump <SRR number> -O output_folder`
Comment: RNA-SEQ
by
GenoMax
126k
If you are trying to re-create an analysis and if it used both SRA# then you will need to get both. If you are simply learning/testing then…
Comment: wrong quality plots in fastqc output
by
poecile.pal
▴ 50
I understood why I got high percentage of duplication. The size of reference was about 150K bp, while I asked for 30M reads with length 151…
Comment: RNA-SEQ
by
ali
• 0
so if I just consider one of the SRR and use fastq-dump --splite -files , its okay ???
Comment: Creating a loop to mark duplicates using Picard
by
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38k
> don't use a loop in a script shell when you can use Snakemake or Nextflow People need to start somewhere. Loops -> xargs/parallel -> sna…
Comment: Mapping paired end reads with ngm and samtools, using prefixes and suffixes for
by
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38k
> what should be the smpl_names.txt That's the file name for the output. Learn more about redirection in linux - Google the term. And yes,…
Comment: Plot heatmap using row_splitting but splitting should based on a column in data
by
Trivas
▴ 630
First, set `show_row_names = FALSE`. You might want to play around with the `col = col_fun` portion of the vignette to change your scale to…
Answer: RNA-SEQ
by
Trivas
▴ 630
Those are replicates, and if you download the SRR files, you should automatically get R1 and R2 for each SRR.
Answer: Creating a loop to mark duplicates using Picard
by
Pierre Lindenbaum
153k
METRICS_FILE="$sbam"/"${bamfile%_sorted.bam}"_metrix instead of METRICS_FILE="$sbam"/"${sbam%_sorted.bam}"_metrix also check the…
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153k
https://ftp.ensembl.org/pub/release-109/variation/gvf/felis_catus/
Comment: Power analysis for patient samples
by
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▴ 120
Sounds good, thanks Jeremy for the help, really appreciate it.
Comment: Power analysis for patient samples
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I think you're doing it right. Since you only have 2 groups, you can use `pwr.t.test`. The default alternative hypothesis is two-sided, b…
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2.1k
Ensembl has a regulatory build for GRCm39: https://ftp.ensembl.org/pub/current_regulation/mus_musculus/ Note that the elements are de…
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3.4k
Wouldn't [liftOver][1] be an option to remap the coordinates to the new assembly? E.g. the [mm10 to mm39][2] chain? [1]: http://hgdownl…
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