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122,211 results • Page
697 of 2445
Sort: Rank
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Votes
Replies
0
votes
0
replies
1.4k
views
Homer annotatePeaks.pl motif density histogram output only showing 0s for motif occurrences
ATAC-seq
Homer
next-gen
ChIP-Seq
motif
4.7 years ago by
rintsen.sherpa
• 0
0
votes
6
replies
9.2k
views
How to keep only Biallelic SNP in vcf
snp
updated 4.7 years ago by
Pierre Lindenbaum
166k • written 4.7 years ago by
wangh920
▴ 10
0
votes
0
replies
1.0k
views
Color nexus tree automatically using associated data
nexus
ape
ggtree
R
python
4.7 years ago by
fhsantanna
▴ 620
1
vote
2
replies
1.6k
views
Handling single-cell RNA-seq data with very few cells and possible conversion to bulk-like RNA-seq
RNA-Seq
updated 4.7 years ago by
ATpoint
90k • written 4.7 years ago by
mb86
• 0
0
votes
0
replies
1.1k
views
Job:
Bioinformatics Curator Positions with Computercraft @ NCBI
sequencing
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
jyu
▴ 90
6
votes
5
replies
4.5k
views
How Do You Align Or Compare Two Networks Content-Wise?
network
graphs
comparison
updated 4.7 years ago by
Biostar
20 • written 15.0 years ago by
Michi
▴ 990
0
votes
0
replies
1.2k
views
Job:
Bioinformatics Data Wrangler with Computercraft @ NCBI
data-wrangler
sequencing
genome
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
jyu
▴ 90
0
votes
1
reply
639
views
Checking sequence similarity between 2 RNAseq samples
RNA-Seq
genome
alignment
sequencing
4.7 years ago by
Triple Nipple
▴ 10
3
votes
1
reply
3.4k
views
How to speed up computeMatrix of deeptools?
software error
updated 4.7 years ago by
opplatek
▴ 300 • written 5.4 years ago by
weiyanjia2008
▴ 30
0
votes
2
replies
826
views
Deseq2 with opposite (dominant negative) design
RNA-Seq
deseq2
R
updated 4.7 years ago by
swbarnes2
15k • written 4.7 years ago by
jack.henry
▴ 50
5
votes
5
replies
2.2k
views
NetNGlyc: input sequence names are not unique: What means?
gene
sequence
glycosilation
site-predictor
updated 4.7 years ago by
Mensur Dlakic
★ 30k • written 4.7 years ago by
mauricio.1313
• 0
1
vote
4
replies
5.2k
views
Interpration of ridgeplot in transcriptomic analysis
RNA-Seq
updated 22 months ago by
Ram
45k • written 4.7 years ago by
javanokendo
▴ 60
4
votes
3
replies
1.8k
views
bowtie2 --passthrough, what does it do???
bowtie2
bowtie
4.7 years ago by
mcrepeau
▴ 20
4
votes
6
replies
4.6k
views
Tools for straightforward visualization of alternative splicing events?
RNA-Seq
Splicing
written 4.7 years ago by
MLN_Bio
▴ 40
2
votes
5
replies
3.9k
views
download all metadata from SRA
SRA
4.2 years ago by
grant.hovhannisyan
★ 2.6k
0
votes
2
replies
2.1k
views
differential binding analysis of cut-tag peak data
ChIP-Seq
updated 4.7 years ago by
rpolicastro
13k • written 4.7 years ago by
17318598206
▴ 30
1
vote
3
replies
1.2k
views
How to identify 2 genes that have highly identical sequence
gene
genome
blastn
gene identification
4.7 years ago by
Ak
▴ 60
2
votes
5
replies
1.6k
views
Gene name put in volcano plot with already have file.
EdgeR
volcano
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
harry
▴ 40
0
votes
2
replies
1.5k
views
refGene Python Api
python api
4.7 years ago by
Bala Hatun
• 0
0
votes
0
replies
894
views
How to create marker file for Gistic?
gene
gistic
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
bioinfo&me
• 0
2
votes
0
replies
2.3k
views
Confusion over SNP strand importance re genotyping (G>C)
taqman
genotyping
strand
dna
SNP
updated 4.7 years ago by
Biostar
20 • written 9.2 years ago by
oooner2014
▴ 20
1
vote
5
replies
2.5k
views
Replicates do not cluster together
r
proteomics
updated 4.7 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
rin
▴ 40
0
votes
0
replies
989
views
Job:
PhD scholarship in bioinformatics in Rostock (Baltic Coast), Germany
aging
nutrition
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
Daniel Palmer
• 0
0
votes
0
replies
594
views
Should one keep softmasking when combining gff+fasta to gbk format?
annotation
4.7 years ago by
robert.murphy
▴ 110
0
votes
0
replies
513
views
Gwas on Window
alignment
updated 4.7 years ago by
Pierre Lindenbaum
166k • written 4.7 years ago by
myintzaw.peter
• 0
0
votes
0
replies
823
views
help regarding loading text files in affy package for background correction
R
affy
textfiles
4.7 years ago by
raavi21198
▴ 20
0
votes
1
reply
672
views
why i don not have peak when use DiffBind
ChIP-Seq
4.7 years ago by
17318598206
▴ 30
1
vote
1
reply
949
views
how to get the best alignment from the sam file
RNA-Seq
alignment
4.7 years ago by
minghuiguo448
• 0
4
votes
2
replies
2.1k
views
R with HPC
R
updated 4.7 years ago by
Friederike
9.0k • written 4.7 years ago by
storm1907
▴ 30
5
votes
3
replies
1.8k
views
How to download RNA files in the easiest way? (from NCBI's SRA)
RNA-Seq
rna-seq
next-gen
sequencing
genome
4.7 years ago by
GoldenRetriever
▴ 40
0
votes
0
replies
1.3k
views
News:
:: FINAL CALL :: Online Course - A Practical Introduction to NGS Data Analysis (April 28 - 30, 2021)
NGS
DNA-Seq
Workshop
Mapping
RNA-Seq
4.7 years ago by
David Langenberger
11k
0
votes
0
replies
1.5k
views
Problems running strelka2
variant calling
ngs
strelka
4.7 years ago by
arne.zibat
• 0
0
votes
0
replies
1.0k
views
Pymol to visualize MSA conservation
alignment
sequence
msa
4.7 years ago by
katamaneni.akhila
• 0
1
vote
0
replies
632
views
The problems of make_html.pl when install the miRDeep2
RNA-Seq
updated 4.7 years ago by
h.mon
35k • written 4.7 years ago by
51203903042
▴ 20
0
votes
0
replies
693
views
Question about a paper called Reference flow: reducing reference bias using multiple population genomes
RNA-Seq
sequence
4.7 years ago by
minghuiguo448
• 0
0
votes
0
replies
1.3k
views
Should I calculate beta diversity with or without rarefaction?
diversity
R
4.7 years ago by
dpc
▴ 250
0
votes
1
reply
2.3k
views
Generate consensus from contig alignment to reference sequence
Assembly
alignment
4.7 years ago by
daewowo
▴ 80
3
votes
1
reply
1.4k
views
What should be the value of Sjdboverhang in STAR?
STAR
index
reference
sjdbOverhang
4.7 years ago by
DareDevil
★ 4.5k
16
votes
13
replies
17k
views
Bash scripting FastQC for multiple fastq files in multiple directories
RNA-Seq
bash
fastQC
updated 4.7 years ago by
DareDevil
★ 4.5k • written 7.1 years ago by
rc1253
▴ 20
0
votes
0
replies
1.3k
views
How maftools oncoplot deal with Splice_Site mutation
maftools
oncoplot
SNV
Splicing
4.7 years ago by
lincaijin1994
▴ 50
1
vote
3
replies
1.3k
views
The problems when i install the miRDeep2
RNA-Seq
4.7 years ago by
51203903042
▴ 20
0
votes
5
replies
1.2k
views
The problems when i map to genome by mapper.pl in miRDeep2
RNA-Seq
4.7 years ago by
51203903042
▴ 20
4
votes
7
replies
1.8k
views
not able to run Deseq 2
RNA-Seq
alignment
sequence
assembly
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
ashwing.kofficial
▴ 10
2
votes
4
replies
1.5k
views
Gene annotations of mammalian genomes
Gene annotation
mammalian genomes
4.7 years ago by
arsala521
▴ 60
0
votes
0
replies
1.4k
views
Deletions are missed from consensus sequence even when they are predominant. Is this common to vcf2fq of vcfutils?
vcf2fq
consensus
bcftools
indel
4.7 years ago by
malaya77
• 0
2
votes
0
replies
1.2k
views
Tool:
New location tracking tool for SARS-CoV-2 variant surveillance
sars-cov-2
variant
covid-19
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
ehaag
▴ 100
3
votes
3
replies
4.9k
views
Playing With Mysql/Ensembl (I): Mapping 'Gene' To 'Xref'
ensembl
mysql
updated 2.1 years ago by
Ram
45k • written 15.7 years ago by
Pierre Lindenbaum
166k
1
vote
2
replies
1.1k
views
Seeking for siRNA screeing data analysis
R
siRNA
gene
Statistic
4.7 years ago by
podderbiswajit4
• 0
8
votes
1
reply
2.0k
views
Tutorial:
Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta
awk
updated 2.7 years ago by
Ram
45k • written 4.7 years ago by
Kevin Blighe
★ 90k
3
votes
5
replies
1.3k
views
conceptual question about paired end sequencing
sequencing
illumina
updated 4.7 years ago by
Ram
45k • written 4.7 years ago by
nhaus
▴ 420
122,211 results • Page
697 of 2445
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Comment: best practice for diploid variant calling
by
Matteo Ungaro
▴ 130
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
Answer: Chip-seq analysis Diffbind
by
ATpoint
90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read
by
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★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
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154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
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Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
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by
samuel.a.odonnell
▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
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Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
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by
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thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
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by
thomas.heigl.ibk
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here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
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3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
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166k
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by
alexandrakortsi
• 0
By sequence. Thank you for your response!
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