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110,306 results • Page
1 of 2207
Sort: Rank
Rank
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Votes
Replies
0
votes
3
replies
278
views
ABySS genome assembler
ABySS
genome
k-mers
assembly
updated 1 hour ago by
shelkmike
▴ 920 • written 2 days ago by
npavliukovec
• 0
0
votes
0
replies
13
views
how to intersect multiple bed files and get results in uncollapsed genomic intervals
bedtools
bedops
intervals
genomic
intersect
1 hour ago by
Alewa
▴ 110
0
votes
1
reply
30
views
Perl. How to extract CDS and gene sequence in a specified interval from GenBank files?
fasta
sequence
perl
GenBank
1 hour ago by
Fungi-Beware!
• 0
0
votes
0
replies
16
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
2 hours ago by
J.F.Jiang
▴ 900
0
votes
2
replies
60
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 1 hour ago by
Ram
39k • written 2 hours ago by
Joel Wallenius
▴ 120
0
votes
3
replies
563
views
Regular Expression for conversion
Linux
grep
updated 42 minutes ago by
ragoce6442
• 0 • written 19 months ago by
shabbas12
▴ 10
0
votes
0
replies
19
views
weird behaviour on bedtools
bedtools
RNA-Seq
2 hours ago by
barrypraveen
▴ 110
1
vote
2
replies
127
views
Retrieving allele-specific information for a variant using VEP annotation
variant-calling
VEP
COSMIC
updated 1 hour ago by
Ram
39k • written 16 hours ago by
bt_cepo
▴ 20
0
votes
1
reply
224
views
[Metagenome assembly] Reassembling bacterial genome using Nanopore contig/reads
illumina
nanopore
assembly
metagenome
updated 3 hours ago by
Ekaterina
• 0 • written 4 weeks ago by
adhamzul
▴ 20
0
votes
1
reply
42
views
IGV grey vs white lines
minimap
nanopore
IGV
updated 2 hours ago by
GenoMax
129k • written 3 hours ago by
Mohd
• 0
0
votes
1
reply
33
views
featureCounts: ERROR: failed to find the gene identifier attribute
gtf
featureCounts
subread
updated 3 hours ago by
GenoMax
129k • written 3 hours ago by
v.berriosfarias
▴ 90
3
votes
4
replies
237
views
6 follow
Unusual FASTQ file
bioinformatics
fastqc
fastq
RNAseq
updated 3 hours ago by
GenoMax
129k • written 18 hours ago by
Nada
• 0
0
votes
2
replies
52
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
2 hours ago by
pg45863
• 0
743
votes
162
replies
113k
views
101 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 weeks ago by
Biostar
1.8k • written 6.5 years ago by
Istvan Albert
98k
0
votes
1
reply
63
views
ABySS Process Killed
ABySS
genome
assembly
updated 3 hours ago by
GenoMax
129k • written 6 hours ago by
asarcillo
• 0
0
votes
0
replies
47
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
6 hours ago by
narges.bioinf
• 0
0
votes
4
replies
460
views
Trimming sequencing primers from reads
trimming
primers
next-gen-sequencing
updated 5 hours ago by
Pierre Lindenbaum
154k • written 5 months ago by
barzilayrom1
▴ 10
2
votes
4
replies
947
views
How to collapse leaves with the same name in ETE3 tree?
collapse
python
ete3
tree
updated 7 hours ago by
susan.klein
▴ 30 • written 23 months ago by
Andrzej Zielezinski
11k
0
votes
1
reply
65
views
Query qbout single cell sequencing
Files
fastq
Data
ScRNA
updated 3 hours ago by
GenoMax
129k • written 8 hours ago by
abbas.waseem.gcu
• 0
0
votes
0
replies
79
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
1 hour ago by
Sun
• 0
0
votes
1
reply
117
views
Why coordinate sort is required in sambamba depths?
sorting
coordinate
sambamba
linux
samtools
updated 15 hours ago by
Pierre Lindenbaum
154k • written 16 hours ago by
MobiusT
▴ 10
0
votes
4
replies
205
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
21 hours ago by
Ahmad
▴ 10
0
votes
1
reply
147
views
Error in download library file in expression console software
expression
microarray
console
updated 13 hours ago by
GenoMax
129k • written 23 hours ago by
Mohammad
• 0
3
votes
2
replies
180
views
ScRNA data
Data
ScRNA
updated 1 day ago by
Dr William Klubinski
▴ 30 • written 1 day ago by
abbas.waseem.gcu
• 0
1
vote
2
replies
161
views
extract all fasta sequence from db v5
blast
protein
updated 1 day ago by
GenoMax
129k • written 1 day ago by
Xylanaser
▴ 80
3
votes
2
replies
247
views
Does the RNAseq data normal if the TPM value 3rd Qutile expression is near 10, but the Max expression are near 20,000
Expression
RNAseq
1 day ago by
alwayshope
▴ 20
0
votes
6
replies
252
views
Demultiplexing bam file
demultiplexing
bam_file
Iontorrent
2 hours ago by
hasani.iut6
▴ 60
1
vote
2
replies
207
views
DEgs RNAseq
RNAseq
1 day ago by
Juan
• 0
1
vote
3
replies
359
views
Counting intronic reads in bulk RNA-seq
rna-seq
updated 1 day ago by
dsull
★ 4.2k • written 2 days ago by
John Ma
▴ 300
0
votes
8
replies
432
views
Single cell chemistry
cell
single
chemistry
just now by
David
• 0
0
votes
0
replies
129
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
download
data
1 day ago by
Vincent Laufer
★ 2.8k
0
votes
7
replies
472
views
Why are some WES VCFs larger than others?
WES
sequencing
genomics
NGS
exome
updated 21 hours ago by
Jeremy Leipzig
21k • written 2 days ago by
Kermit
▴ 80
0
votes
4
replies
321
views
SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
snakemake
1 day ago by
Dhatri Badri
• 0
0
votes
1
reply
198
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 21 hours ago by
Fabio Marroni
★ 3.0k • written 1 day ago by
1362321710
• 0
0
votes
1
reply
183
views
DownsampleSam
picard
DownsampleSam
updated 1 day ago by
Pierre Lindenbaum
154k • written 1 day ago by
mathalfilip
• 0
0
votes
1
reply
192
views
Error while running Megahit
Megahit
updated 1 day ago by
Mensur Dlakic
★ 23k • written 2 days ago by
abhiramiabhirami9072
• 0
0
votes
2
replies
266
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
12 hours ago by
Camilo Andres
▴ 30
1
vote
5
replies
337
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
updated 2 days ago by
GenoMax
129k • written 2 days ago by
DanielEB_fisk
• 0
0
votes
0
replies
170
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
2 days ago by
dima
• 0
1
vote
0
replies
223
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics
single-cell
RNA
DEG
2 days ago by
abbas89
▴ 10
0
votes
3
replies
353
views
metric informing about the similarity of gene lists in OrderedList
orderedlist
updated 2 days ago by
Vincent Laufer
★ 2.8k • written 4 days ago by
kkolmus
• 0
18
votes
6
replies
6.5k
views
VCF header line counting
vcf
header
updated 2 days ago by
beausoleilmo
▴ 530 • written 8.3 years ago by
basalganglia
▴ 40
0
votes
1
reply
198
views
How extract specific SNP position from the bed file-Bedtools
bedtools
for
Help
updated 2 days ago by
GenoMax
129k • written 2 days ago by
rbaranikumar
• 0
0
votes
0
replies
592
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure
pymol
protein
pdb
python
2 days ago by
Aatif Hashmi
• 0
2
votes
5
replies
432
views
Design matrix to remove technical replicate effect
edgeR
2 days ago by
ARD
▴ 10
0
votes
1
reply
278
views
Deferentially expressed gene with high log2foldchange by DESeq2; but not meaningful at the individual level
DESeq2
RNA-seq
DGEA
updated 2 days ago by
Vincent Laufer
★ 2.8k • written 3 days ago by
Sara
▴ 10
1
vote
2
replies
232
views
Abyss taking a Long time to run
abyss
assembly
genome
fastq
3 days ago by
Maliha
▴ 20
0
votes
2
replies
253
views
Import or read Snapgene .dna files into R
R
.dna
snapgene
2 days ago by
eggrandio
▴ 40
2
votes
2
replies
252
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 2 days ago by
Istvan Albert
98k • written 3 days ago by
antoine.fauchois92
▴ 20
0
votes
3
replies
338
views
Biological replicates in RNA-seq
RNA-seq
biological-replicates
updated 3 days ago by
mark.ziemann
★ 1.8k • written 3 days ago by
Mars
• 0
110,306 results • Page
1 of 2207
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Comment: Bioinformatics Master's Student
Ribo-Seq Analysis
Answer: Retrieving allele-specific information for a variant using VEP annotation
Comment: addModuleScore and enrichment score methods
addModuleScore and enrichment score methods
C: miRNA differential expression
Answer: Bioinformatics Master's Student
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Recent Replies
Answer: ABySS genome assembler
by
shelkmike
▴ 920
You can use Kmergenie (http://kmergenie.bx.psu.edu/). It is a special tool for finding the optimal k-mer length.
Comment: Retrieving allele-specific information for a variant using VEP annotation
by
Ram
39k
It is pretty trivial to do the COSMIC annotation without tools such as VEP - download their coding and non-coding VCFs, normalize (decompos…
Answer: Perl. How to extract CDS and gene sequence in a specified interval from GenBank
by
Fungi-Beware!
• 0
Figured I need to attach an expected OUTPUT result. Should look something like this: ---------- ``` LOCUS 19 58617616 bp DNA HTG 23-NOV-2…
Comment: Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
by
Joel Wallenius
▴ 120
Yes, well... surely it's better with some FPs and TPs than nothing at all, eh. Is there another way to do this? Hmm...
Comment: Demultiplexing bam file
by
hasani.iut6
▴ 60
No. All of the Ids are "13.02.1402_POOL2". Do you think my bam file is not correct?
Comment: Demultiplexing bam file
by
hasani.iut6
▴ 60
Yes, you're right, I know the bam file consists of multiple samples (It should be between 30 to 40 samples) and the size of the bam file is…
Comment: Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
by
ATpoint
72k
Technically you can mask it, but what if the variant comes from the pseudogene and not the gene you "want"?
Answer: Regular Expression for conversion
by
ragoce6442
• 0
Here is the simple guide for [Javascript][1], if you would like to give it a look. [1]: [1]: https://techindetail.com/javascript/
Answer: Retrieving allele-specific information for a variant using VEP annotation
by
Joel Wallenius
▴ 120
My interpretation of the documentation is that no, you can't have the specific COSMIC id, because of that licensing whatchamacallit.
Comment: fgsea/clusterProfiler Packages for nCounter data enrichment analysis
by
pg45863
• 0
Hello Meisam. Understood! thank you
Answer: [Metagenome assembly] Reassembling bacterial genome using Nanopore contig/reads
by
Ekaterina
• 0
Take a look at the stRainy. Keep in mind that it is still under development and has not been tested on real data https://github.com/kater…
Comment: IGV grey vs white lines
by
GenoMax
129k
You should be filtering on field 5 in SAM file that is for mapping quality (MAPQ). As noted above any read that is multi-mapped should have…
Comment: fgsea/clusterProfiler Packages for nCounter data enrichment analysis
by
Meisam
▴ 170
It is not clear what you mean by "neither provided me with the understandable results". Do they give you error? Then what error. Do they gi…
Comment: featureCounts: ERROR: failed to find the gene identifier attribute
by
GenoMax
129k
A GTF file should not be a table unless you mean it in a loose sense. It should be a file with lines containing tabular fields. At a minimu…
Comment: ABySS Process Killed
by
GenoMax
129k
> I am now thinking that my PC's 16 Gb RAM is not enough That is more than likely. See: https://www.biostars.org/p/295032/#295238
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