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538 results • Page
2 of 11
Sort: Votes
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Views
Votes
Replies
2
votes
5
replies
414
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
6 days ago by
DanielEB_fisk
• 0
2
votes
3
replies
1.2k
views
mutational signatures in different tumor samples
somatic mutation
mutational signature
updated 3 days ago by
Vincent Laufer
★ 2.9k • written 4.4 years ago by
lzy
▴ 20
2
votes
1
reply
199
views
P values on box plots
sequencing
Statistics
RNA
updated 24 days ago by
Basti
★ 1.5k • written 24 days ago by
Abdullah
▴ 10
2
votes
1
reply
1.8k
views
How do I apply a patch to hg38?
reference
human
freeze
hg38
patch
updated 3 days ago by
Jeremy Leipzig
21k • written 5.6 years ago by
imperialcommando117
• 0
2
votes
5
replies
443
views
How to check a gene in an open chromatin region or not?
ATAC-seq
27 days ago by
Chris
▴ 100
2
votes
3
replies
314
views
Low mapping percentage
mapping
STAR
RNAseq
1 day ago by
Sib
▴ 40
2
votes
2
replies
304
views
DESeq factor order
DESeq2
17 days ago by
Chris
▴ 10
2
votes
3
replies
862
views
Freebayes command stopped due to lack of space
freebayes
SNP-calling
updated 11 days ago by
Ram
39k • written 5.0 years ago by
amcheroo
• 0
2
votes
6
replies
380
views
Find data-based Gene_IDs for unknown gene_IDs in gtf.file
RNA-SEQ
annotation
GO-term
14 days ago by
Pegasus
▴ 90
2
votes
6
replies
1.0k
views
Time series RNA seq design query
RNA-seq
time-series
deseq2
updated 5 days ago by
Ram
39k • written 18 months ago by
kra277
• 0
2
votes
3
replies
271
views
Using RNA-seq to detect pathogen sequences in host tissue
RNA-seq
11 days ago by
erik.burchard
▴ 10
2
votes
2
replies
392
views
Online tool for creating figures of gene with its features
features
genes
figures
updated 16 days ago by
Ram
39k • written 6 months ago by
andre.arrudalima
▴ 20
2
votes
8
replies
2.6k
views
How to convert a database from protein to nucleotide
blastn
unix
blastx
blast
updated 24 days ago by
Ram
39k • written 6.2 years ago by
AJTrunkskun94
• 0
2
votes
7
replies
1.5k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence
ncbi
gene
genbank
updated 13 days ago by
Ram
39k • written 5.2 years ago by
navela78
▴ 70
2
votes
5
replies
389
views
RNA SEQ reads assembly for illumina sequenced data
NGS
linux
nanopore
updated 25 days ago by
Ram
39k • written 5 weeks ago by
Adyasha
• 0
2
votes
3
replies
339
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
25 days ago by
Dan
▴ 120
2
votes
1
reply
198
views
'Seurat' package
Seurat
R
updated 25 days ago by
Ram
39k • written 25 days ago by
sooni
• 0
2
votes
1
reply
266
views
scRNAseq (bioconductor) data to seurat object
bioconductor
seurat
scRNAseq
updated 18 days ago by
ATpoint
72k • written 18 days ago by
Alex
▴ 20
2
votes
0
replies
215
views
Reference request for getting the big picture of gene taxonomy
genes
textbook
16 days ago by
garbagelister
▴ 20
2
votes
0
replies
797
views
how to find the bound form of an enzyme structure?
enzyme
updated 23 days ago by
Ram
39k • written 6.0 years ago by
lochanamp
▴ 70
2
votes
2
replies
181
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 3 days ago by
Dr William Klubinski
▴ 80 • written 4 days ago by
linnet.roque6
▴ 10
2
votes
4
replies
607
views
DESeq2 batch effects with nonuniform design matrix
DESeqDataSet
DESeq2
batch
updated 23 days ago by
Ram
39k • written 12 months ago by
mcsimenc
▴ 20
2
votes
4
replies
234
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 4 days ago by
Ram
39k • written 4 days ago by
miguellarrazlopezdenovales
• 0
2
votes
2
replies
111
views
how to use Hemtools bed2vcf?
vcf
linux
conversion
bed
updated 6 days ago by
Pierre Lindenbaum
154k • written 6 days ago by
MobiusT
▴ 10
2
votes
3
replies
690
views
Including bioinformatics into an agriculture/horticulture dissertation project
agrobioinformatics
plant-gene-analysis
updated 5 days ago by
Ram
39k • written 4.1 years ago by
cipri91rusu
• 0
2
votes
3
replies
378
views
Samtools faidx can't be run in succession on two reference files?
Samtools
22 days ago by
DdogBoss
• 0
2
votes
0
replies
724
views
Why are there multiple bax/fastq files associated with my PacBio run?
genome
PacBio
WGS
sequencing
updated 5 days ago by
Ram
39k • written 4.1 years ago by
nickvpinkham
▴ 20
1
vote
4
replies
1.5k
views
Time series event recurrence comparison
recurrence
time-series
updated 5 days ago by
Ram
39k • written 6.7 years ago by
Nicolas Rosewick
10k
1
vote
0
replies
1.2k
views
Align two single cell experiments
R
single-cell
updated 10 days ago by
Ram
39k • written 4.5 years ago by
elb
▴ 230
1
vote
2
replies
217
views
multi-mapping reads settings in Rsubread or Rsubjunc
Rsubjunc
RNA-seq
19 days ago by
xiaoleiusc
▴ 120
1
vote
0
replies
1.3k
views
NCBI Taxon ID to IMG Genome IDs
taxon
html
updated 3 days ago by
Ram
39k • written 3.9 years ago by
Mohak
▴ 20
1
vote
6
replies
570
views
DESeq2
heatmap
R
DESeq2
27 days ago by
Nelo
• 0
1
vote
2
replies
1.6k
views
Learning some Drop-Seq as a first approach to RNA-Seq while on vacation
hardware
RNA-Seq
drop-seq
updated 20 days ago by
Ram
39k • written 5.8 years ago by
Anima Mundi
★ 2.9k
1
vote
2
replies
176
views
sorting BAM file
BAM
updated 5 days ago by
ATpoint
72k • written 5 days ago by
Mohammad Amin
• 0
1
vote
1
reply
184
views
UMI extract and deup
UMIs
24 days ago by
samuel
▴ 230
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna
cuffdiff
updated 11 days ago by
Ram
39k • written 4.7 years ago by
sbb
▴ 10
1
vote
8
replies
860
views
Betacoronavirus.00.nsq error
corona
biostars
updated 20 days ago by
Ram
39k • written 16 months ago by
Sam
• 0
1
vote
0
replies
1.2k
views
sequence alignment using edlib c++ library
cpp
alignment
updated 13 days ago by
Ram
39k • written 4.8 years ago by
BDK_compbio
▴ 140
1
vote
4
replies
4.9k
views
Conditionally coloring the fold change values to plot a heatmap using pheatmap
R
heatmap
updated 16 days ago by
Ram
39k • written 5.3 years ago by
chetana
▴ 60
1
vote
1
reply
508
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 3 days ago by
GenoMax
129k • written 3 days ago by
Mohd
▴ 20
1
vote
2
replies
292
views
Identifying/Annotating Enhancers
enhancer
R
ENCODE
bedtools
updated 12 days ago by
ATpoint
72k • written 12 days ago by
cthangav
▴ 40
1
vote
4
replies
962
views
Simulate the sequence data
next-gen-sequencing
genetics
updated 13 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
1
vote
1
reply
928
views
microarray data handling
R
microarray
updated 17 days ago by
Ram
39k • written 5.5 years ago by
vincent.bioscience
• 0
1
vote
0
replies
134
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
3 days ago by
abba647
▴ 10
1
vote
1
reply
362
views
Cellranger count fails at chunks_read stage
cellranger
updated 23 days ago by
Ram
39k • written 13 months ago by
dtran822
• 0
1
vote
1
reply
990
views
cfDNA target seq vs. cfDNA WES
cfDNA
updated 11 days ago by
Ram
39k • written 4.9 years ago by
genetic
▴ 40
1
vote
0
replies
2.5k
views
Running Multiple Alignments in MEGA with a script produces errors.
next-gen
RNA-Seq
MEGA
multiple-alignment
updated 19 days ago by
Ram
39k • written 7.2 years ago by
rachelrodgers12
▴ 10
1
vote
3
replies
702
views
Regular Expression for conversion
Linux
grep
updated 5 days ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
1
vote
10
replies
2.6k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 9 days ago by
Ram
39k • written 4.2 years ago by
Kumar
▴ 100
1
vote
0
replies
116
views
mirdeep2- unable to extract files for mapping -extract_miRNAs: command not found error
miRNA
miRDeep2
miRNAanalysis
26 days ago by
Supernova
• 0
538 results • Page
2 of 11
Recent Votes
Answer: How to calculate TPM from featureCounts output
A: Problem regarding Software installation.
Answer: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
How To Predict Pseudogenes In A Genome
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Recent Replies
Answer: Getting species names and taxa id from assembly accession number
by
MirianT_NCBI
▴ 580
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
Answer: Installation of PPFinder
by
GenoMax
129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output
by
rpolicastro
12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl
by
ATpoint
72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin
by
sativus
• 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis
by
nux
▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
Comment: CNNScoreVariants Error
by
bestone
▴ 10
Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG
by
jrodrigu
• 0
Thank you so much. I made the suggested changes. However, I still have the same problem. Please check the new log file. https://github.c…
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation"
by
bioinfo_ga
▴ 50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output
by
bioinfo_ga
▴ 50
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
biofalconch
▴ 580
Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
by
biofalconch
▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file
by
kirillkirilenko
▴ 10
It works, thank you!
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