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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
0
votes
21
replies
2.8k
views
HTSeq-Count: no_feature too high?
htseq-count
19 months ago by
sea.joson
▴ 10
7
votes
21
replies
3.2k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.5 years ago by
jmsyl.hong
• 0
5
votes
20
replies
4.2k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 19 months ago by
Ram
43k • written 8.7 years ago by
Hans
▴ 140
6
votes
20
replies
6.4k
views
filling of missing genotype information in merged variant call vcf file
SNP
5.9 years ago by
princy149
▴ 80
4
votes
20
replies
1.9k
views
How can I count aminoacid residues from a HUGE compressed fasta file?
sequence
4.4 years ago by
schlogl
▴ 160
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper
RNA-seq
7 months ago by
langziv
▴ 50
8
votes
20
replies
3.0k
views
Why does cufflinks split this transcript?
RNA-Seq
cufflinks
assembly
6.4 years ago by
corend
▴ 70
9
votes
20
replies
4.4k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 14 months ago by
Ram
43k • written 5.8 years ago by
marongiu.luigi
▴ 710
22
votes
20
replies
2.6k
views
what is the prefered strategy to treat with blast-less transcriptomes from RNA-seq
blast
RNA-Seq
genome
gene
updated 13 months ago by
Ram
43k • written 7.8 years ago by
Farbod
★ 3.4k
5
votes
20
replies
8.4k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.8 years ago by
varsha619
▴ 90
2
votes
20
replies
2.4k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
8 months ago by
Maxine
▴ 40
8
votes
20
replies
2.7k
views
Getting read depth for normal and tumour
R
WGS
vcf
5.1 years ago by
zizigolu
★ 4.3k
8
votes
20
replies
2.5k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 24 months ago by
Ram
43k • written 5.8 years ago by
Bara'a
▴ 270
6
votes
19
replies
2.9k
views
Clustering for Single-cell RNA-seq Data
clustering
R
single-cell
4.8 years ago by
aloke205
▴ 40
3
votes
19
replies
1.6k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS
error
panels
sequencing
updated 10 months ago by
Asaf
10k • written 10 months ago by
captainlabman
▴ 20
18
votes
19
replies
2.3k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 17 months ago by
Ram
43k • written 5.4 years ago by
rbkh09
• 0
4
votes
19
replies
3.2k
views
Use machine learning as classifier
R
rRNA
16S
18S
ITS
updated 6.7 years ago by
Biostar
20 • written 6.9 years ago by
cool.abbecker
▴ 30
9
votes
19
replies
2.4k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.3 years ago by
schlogl
▴ 160
0
votes
19
replies
1.4k
views
map fasts files
RNA-Seq
FASTQ
R
6.3 years ago by
Learner
▴ 280
17
votes
19
replies
2.8k
views
Sorting sequences according header
software error
sequence
Assembly
next-gen
7.7 years ago by
Gian77
▴ 60
5
votes
19
replies
1.7k
views
how I can come up with a permanent error
R
software error
7.1 years ago by
zizigolu
★ 4.3k
15
votes
19
replies
1.9k
views
trimmomaric command for a fasta file?
trimmomatic
updated 6.0 years ago by
Ram
43k • written 6.0 years ago by
Nadin.asal
• 0
0
votes
19
replies
2.0k
views
scatterplot in R
microarray
expression
gene
updated 19 months ago by
Ram
43k • written 19 months ago by
bioinformatics
▴ 40
5
votes
19
replies
4.1k
views
8 follow
Hisat2 aligner problem
RNA-Seq
ChIP-Seq
alignment
Assembly
software error
updated 4 months ago by
ATpoint
82k • written 5.0 years ago by
ta_awwad
▴ 340
3
votes
19
replies
6.2k
views
gatk-launch file missing
next-gen
sequencing
software error
updated 5.0 years ago by
finswimmer
16k • written 5.0 years ago by
sruthi
▴ 40
1
vote
19
replies
919
views
Matching transcriptomic data to clinical data
R
updated 3 months ago by
Ram
43k • written 3 months ago by
Azra
▴ 10
7
votes
19
replies
3.0k
views
mapping script process sleeping on server.
alignment
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
lvogel
▴ 30
22
votes
19
replies
3.2k
views
targets of a list of miRNAs
miRNAs
RNA-Seq
DEanalysis
target-prediction
7.6 years ago by
zizigolu
★ 4.3k
10
votes
19
replies
3.5k
views
What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
Genebank
blast
UniProt
updated 3.0 years ago by
GenoMax
142k • written 3.0 years ago by
matt
▴ 20
6
votes
19
replies
1.7k
views
Fastq header modification
sequence
next-gen
updated 6.2 years ago by
Ram
43k • written 6.2 years ago by
Guillaume
• 0
0
votes
19
replies
3.9k
views
Difficulty installing GATKtoolkit
GATK
Variant calling
SNPs
Indels
6.4 years ago by
jaqx008
▴ 110
1
vote
19
replies
7.1k
views
Conda install package - different internals
R
software error
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
lihe.liu
▴ 30
0
votes
19
replies
2.8k
views
error related to vcfstats
numpy
snp
vcf
vcfstats
2.8 years ago by
rheab1230
▴ 140
0
votes
19
replies
1.6k
views
best blast strategy: read vs cluster?
alignment
blast
search
strategy
4.4 years ago by
marongiu.luigi
▴ 710
7
votes
19
replies
7.1k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray
R
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
mheiser1
▴ 10
13
votes
19
replies
5.4k
views
bbmerge not joining paired-end reads
bbmerge
alignment
6.5 years ago by
bioplanet
▴ 60
0
votes
19
replies
9.6k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.9 years ago by
seta
★ 1.9k
1
vote
19
replies
2.1k
views
High no feature counts in ht-seq counts
RNA-Seq
sequencing
5.4 years ago by
eozcan
▴ 10
2
votes
18
replies
6.3k
views
No differentially expressed genes using DESeq2
RNA-Seq
deseq2
7.5 years ago by
Sumit Paliwal
▴ 40
2
votes
18
replies
2.4k
views
I need help in this
gene
weblems
alignment
updated 21 months ago by
Ram
43k • written 8.4 years ago by
efosa15
• 0
4
votes
18
replies
17k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.5 years ago by
Biostar
20 • written 5.8 years ago by
Shelle
▴ 30
2
votes
18
replies
1.7k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
6 weeks ago by
b.contreras.moreira
▴ 200
3
votes
18
replies
1.9k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
19 months ago by
lacb
▴ 120
0
votes
18
replies
1.8k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 8 months ago by
GenoMax
142k • written 9 months ago by
Apex92
▴ 280
1
vote
18
replies
1.8k
views
Find tissues that are functionally related
tissue
functionally-related
gene-expression
updated 4.7 years ago by
Biostar
20 • written 4.7 years ago by
Natasha
▴ 40
4
votes
18
replies
3.0k
views
Inline barcodes in the reverse reads
barcodes
7.6 years ago by
Picasa
▴ 640
0
votes
18
replies
1.7k
views
No gene name after annovar vcf file processing
vcf
annovar
4.6 years ago by
valerie
▴ 100
7
votes
18
replies
8.6k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
hana
▴ 190
7
votes
18
replies
5.0k
views
Fold change UP and Down in dplyr calculation
R
6.8 years ago by
1769mkc
★ 1.2k
7
votes
18
replies
4.6k
views
Bowtie indexing of a fasta file that consists of a large amount of sequences
bowtie
alignment
genome
7.6 years ago by
valerie
▴ 100
1,000 results • Page
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Recent Votes
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
C: Snakemake vs. Nextflow: strengths and weaknesses
Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
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Recent Awards •
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Scholar
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Pierre Lindenbaum
161k
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▴ 30
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★ 2.5k
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Muhammad
• 0
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▴ 100
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed
by
m13113153781
• 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
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