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122,209 results • Page
692 of 2445
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Votes
Replies
3
votes
7
replies
4.4k
views
How to calculate frequencies of SNPs with respect to a particular allele by plink?
frequency
snp
plink
4.7 years ago by
jamespower
▴ 100
0
votes
0
replies
1.6k
views
Job:
Staff Data Scientist / Bioinformatician in Proteomics at Max Perutz Labs Vienna
proteomics
massspectrometry
4.7 years ago by
Markus
• 0
0
votes
11
replies
3.1k
views
bbmap for FAIRE-seq and other line than reference
aligner
mapping
sequencing
4.7 years ago by
boczniak767
▴ 880
0
votes
1
reply
1.6k
views
What does the -0 flag of samtools fastq mean?
samtools
updated 4.7 years ago by
aw7
▴ 390 • written 4.7 years ago by
O.rka
▴ 750
2
votes
4
replies
1.6k
views
How to grep every row for the every value of a column?
RGeneID
4.7 years ago by
markgodek
▴ 50
1
vote
0
replies
1.5k
views
Analysing chromHMM output to get the correlation of binding patterns of interrogated DNA binding factors
pipeline
general
4.7 years ago by
munaj86
▴ 30
3
votes
3
replies
2.0k
views
How to merge several BED files to create a comprehensive overview file
pandas
granges
python
bioconductor
updated 4.7 years ago by
Jorge Amigo
14k • written 4.7 years ago by
Jordi
▴ 60
0
votes
0
replies
734
views
GEMINI (GEnome MINIng) inheritance pattern command warning no affecteds in family 0
ubuntu
GEnomeMINIng
gemini
4.7 years ago by
taniamahmood38
▴ 60
0
votes
0
replies
598
views
Tped file locus column to gene
plink
4.7 years ago by
storm1907
▴ 30
19
votes
11
replies
21k
views
6 follow
Get Gene Symbol Synonyms/Aliases With Biomart
biomart
gene
updated 4.7 years ago by
ATpoint
90k • written 14.0 years ago by
Caddymob
★ 1.0k
2
votes
4
replies
1.9k
views
Trimmomatic not recognising both adapters
trimmomatic
adapters
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
OhHiImNewHere
▴ 10
0
votes
1
reply
771
views
How to convert a value of columnA to a value of columnB (in R)?
R
updated 4.7 years ago by
cpad0112
21k • written 4.7 years ago by
kelly.wang135
▴ 70
0
votes
0
replies
736
views
Error in cut edge program in MATLAB
function
programming
4.7 years ago by
Abhinav
• 0
0
votes
1
reply
931
views
what is the difference between cell lines and tissue when doing sequencing analysis
dna
mapping
sequence
updated 4.7 years ago by
GenoMax
154k • written 4.7 years ago by
charlie
• 0
0
votes
0
replies
794
views
The number of predicted CDS/ORF does not match with the annotated ones (KEGG-GHOSTKOALA)
gene
KEGG
alignment
rna
genomics
4.7 years ago by
shail.nair05
▴ 20
1
vote
1
reply
1.6k
views
Understanding blast2go annotation result
combinedGOgraph
annotation
blast2go
updated 4.7 years ago by
Istvan Albert
103k • written 4.7 years ago by
Kash
▴ 110
4
votes
3
replies
4.8k
views
How to remove multiple adapter sequences by Cutadapt
RNA-seq
cutadapt
adapter
multipleadapters
updated 4.7 years ago by
cpad0112
21k • written 4.7 years ago by
okiedokie1208
▴ 40
0
votes
4
replies
2.2k
views
Computing Hamming similarity (opposite of distance) between string P and each position in string T
alignment
scoring
programming
4.7 years ago by
lehuyduc3
• 0
1
vote
2
replies
1.4k
views
How can I get GTF file for TE annotations from Helicoverpa armigera?
genome
workflow
database
pipeline
4.7 years ago by
pavelasquezv
▴ 50
1
vote
1
reply
1.1k
views
Interpret Bedtools Overlap?
bed
updated 4.7 years ago by
Istvan Albert
103k • written 4.7 years ago by
kstangline
▴ 110
2
votes
3
replies
2.8k
views
Is there a way to convert rpkm data to raw counts
rna
4.7 years ago by
rishav513
▴ 30
11
votes
10
replies
23k
views
ENSMUSG number convert to gene name
ensembl
gene
updated 3.0 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
yueli7
▴ 250
9
votes
4
replies
17k
views
Interpretation of Principal component analysis
clustering
updated 4.7 years ago by
Mensur Dlakic
★ 30k • written 4.7 years ago by
xqyn
▴ 60
8
votes
9
replies
8.4k
views
8 follow
Issue With CRAM -> BAM -> FASTQ Conversion
samtools
fastq
cram
bam
view
updated 2.6 years ago by
Michael
• 0 • written 6.4 years ago by
denis.k
▴ 20
0
votes
0
replies
1.2k
views
bootstrapping genomes for demographic analysis
bootstrapping
genome
bootstrap
demography
4.7 years ago by
truebeliever24
▴ 50
0
votes
0
replies
883
views
Combine populations.samples.fa alleles using STACKS
rad
snp
haplotype
vcf
updated 4.7 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
mr.two
• 0
3
votes
3
replies
1.7k
views
MACS2
mapping
updated 4.7 years ago by
ATpoint
90k • written 4.7 years ago by
snehu.sambare
▴ 10
1
vote
2
replies
1.4k
views
Clustering two different RNA-seq timeseries results to identify shared/opposite gene patterns?
RNA-seq
clustering
time-series
updated 2.5 years ago by
Ram
45k • written 4.7 years ago by
kelen
▴ 210
2
votes
6
replies
3.2k
views
Modify chromosome column in bam file using pysam fetch
pysam
updated 4.7 years ago by
David Parry
▴ 170 • written 4.7 years ago by
Linda
▴ 80
0
votes
0
replies
841
views
Quality checking phasing
vcf
shapeit
phasing
4.7 years ago by
truebeliever24
▴ 50
242
votes
176
replies
118k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 2.5 years ago by
Ram
45k • written 10.3 years ago by
TriS
★ 4.8k
0
votes
0
replies
2.0k
views
Job:
Postdoctoral Fellowship – Machine Learning for Drug Discovery at University of Connecticut
drugdiscovery
machinelearning
systembiology
4.7 years ago by
Minghu
• 0
0
votes
1
reply
896
views
How to establish cellular localisation of a protein using STRING?
visualization
ppi
stringdb
cytoscape
updated 4.7 years ago by
Scooter
▴ 310 • written 4.7 years ago by
kz
• 0
1
vote
4
replies
4.1k
views
Annotate Ref/Alt for a list of rsIDs?
dbSNP
snp
updated 4.7 years ago by
GenoMax
154k • written 8.2 years ago by
blazer9131
▴ 20
1
vote
4
replies
1.4k
views
is it possible to extract all the exome information from WGS?
genome
sequencing
updated 4.7 years ago by
Michael
56k • written 4.7 years ago by
Hyper_Odin
▴ 320
0
votes
0
replies
704
views
How to handle mouse events in PyMOL plugins
PyMOLplugin
events
PyMOL
4.7 years ago by
d.s.molodenskiy
• 0
0
votes
0
replies
676
views
is the absolute value of `plink2.eigenvec.var` from `plink2 --pca biallelic-var-wts approx` a measure of how much each SNP drives PCS?
plink
4.7 years ago by
curious
▴ 900
1
vote
1
reply
2.4k
views
Autodock parse error
autodockautodock_vina
updated 4.7 years ago by
tothepoint
▴ 940 • written 4.7 years ago by
evashan96
• 0
2
votes
3
replies
1.2k
views
Gene Expression
python
protein
updated 4.7 years ago by
Kevin Blighe
★ 90k • written 4.7 years ago by
12art
• 0
4
votes
5
replies
7.0k
views
VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
GATK
updated 4.7 years ago by
BunnyBosZ
• 0 • written 7.3 years ago by
Ana
▴ 200
4
votes
2
replies
2.7k
views
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 92283: Duplicate allele added to VariantContext: C, …
VariantsToTable
vcf
gatk
4.7 years ago by
DareDevil
★ 4.5k
6
votes
3
replies
1.5k
views
Illumina Terminology Clarification
genomics
updated 4.7 years ago by
Mensur Dlakic
★ 30k • written 4.7 years ago by
joe_genome
▴ 70
0
votes
0
replies
1000
views
Job:
Cancer Bioinformatician @ University of East Anglia - Norwich Medical School UK
uk
cancer
postdoc
4.7 years ago by
dan.brewer
▴ 120
0
votes
2
replies
3.2k
views
FindIntegrationAnchors returs 0 anchor after filtering
seurat
dataintegration
FindIntegrationAnchors
4.7 years ago by
mbk0asis
▴ 700
0
votes
5
replies
2.5k
views
How to convert physical position to genetic position given 1cM = 1Mb?
IBDLD
geneticmap
updated 4.7 years ago by
Pierre Lindenbaum
166k • written 4.7 years ago by
GiantSilverSoy
▴ 130
0
votes
7
replies
2.4k
views
I have multiple read count files in txt format, I don't know how to merge them all in a single file
rnaseqR
4.7 years ago by
rishav513
▴ 30
0
votes
0
replies
691
views
Single end or paired end LP WGS
alignment
mapping
sequencing
genomics
4.7 years ago by
am
▴ 70
12
votes
14
replies
11k
views
STAR alignment command.
RNA-Seq
alignment
sequence
assembly
rna-seq
updated 4.7 years ago by
DareDevil
★ 4.5k • written 7.4 years ago by
amitunited0532
▴ 40
5
votes
6
replies
4.1k
views
noisy chip-seq peaks
deeptools
macs2
chip-seq
peaks
igv
updated 4.7 years ago by
jared.andrews07
★ 19k • written 4.7 years ago by
kolikolmakani14
• 0
1
vote
2
replies
2.3k
views
Select one variant from multiple in ALT in VCF file
VCF
Filter
multiplevariants
WGS
updated 4.7 years ago by
Medhat
9.8k • written 4.7 years ago by
FL512
▴ 20
122,209 results • Page
692 of 2445
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zizigolu
★ 4.4k
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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
cmdcolin
★ 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.
Comment: ID unifiying across different datasets
by
GenoMax
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
by
Wu-Sheng Zhang
▴ 10
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
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…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
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…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
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
by
Pierre Lindenbaum
166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
alexandrakortsi
• 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
xinguok794
▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
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