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Limit : this week
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228 results • Page
1 of 5
Sort: replies
Rank
Views
Votes
Replies
362
votes
82
replies
143k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 2 days ago by
jena
▴ 290 • written 11.1 years ago by
ole.tange
★ 4.4k
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 3 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
5
votes
15
replies
4.7k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 5 days ago by
vague-barracuda-4686
• 0 • written 4.7 years ago by
Apprentice
▴ 160
12
votes
14
replies
2.4k
views
8 follow
Forum:
Recovering bam files after unknown deletion in the storage
photorec
bam
sequencing
written 4.8 years ago by
Gabriel Wajnberg
▴ 70
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 2 days ago by
Ram
43k • written 13.5 years ago by
toshnam
▴ 650
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 21 hours ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
6
votes
13
replies
469
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
2 days ago by
Maverick
▴ 10
1
vote
13
replies
964
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 2 days ago by
lcj34
▴ 410 • written 9 days ago by
b.contreras.moreira
▴ 70
0
votes
12
replies
769
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
2 days ago by
biwdpang
• 0
2
votes
12
replies
374
views
Variant calling of GBS data
GBS
variants
BQSR
5 hours ago by
analyst
▴ 10
3
votes
12
replies
631
views
Facing problem with extracting phenotypic data from GEO
WGCNA
GEO
1 day ago by
bioinfo_enthusiast
• 0
1
vote
12
replies
438
views
Nanopore data filtering using fastp
fastp
nanopore
just now by
emilydolivo97
• 0
4
votes
12
replies
3.4k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 2 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 1 day ago by
Tania
• 0 • written 6.8 years ago by
Tom_L
▴ 350
2
votes
11
replies
802
views
RNA seq aligner?
Alignment
3 days ago by
tesfaye
• 0
4
votes
11
replies
1.2k
views
Paired layout, but one fastq file
fastq
updated 12 hours ago by
GenoMax
140k • written 12 months ago by
Andy
▴ 120
15
votes
10
replies
7.5k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 20 hours ago by
Alex Reynolds
35k • written 8.2 years ago by
int11ap1
▴ 470
2
votes
10
replies
697
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 1 hour ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
3
votes
10
replies
653
views
Intersect gene IDs list and GFF3 to get the annotation.
annotation
GFF
5 days ago by
Lissa Cruz Saavedra
• 0
0
votes
9
replies
452
views
Intersect genomic locations with genes
fanc
Chromatin
conformation
Hic
hic
updated 6 days ago by
zx8754
11k • written 6 days ago by
naveedhasan2000
• 0
1
vote
9
replies
157
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 10 minutes ago by
GenoMax
140k • written 4 hours ago by
Lila M
★ 1.2k
0
votes
9
replies
445
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 3 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
4
votes
9
replies
667
views
Snakemake >= version 8 cluster configuration and SLURM job submission
parallelization
slurm
snakemake
cluster
updated 2 days ago by
Simon
▴ 10 • written 6 days ago by
Maxwell
▴ 20
6
votes
9
replies
1.7k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
1 day ago by
Zeng Jingyu
▴ 60
5
votes
8
replies
2.2k
views
VariantCalling with single sanger read
snps
blast
indel
Variant-Calling
updated 2 days ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
0
votes
8
replies
405
views
STAR aligner options
STAR
5 hours ago by
theophile
• 0
2
votes
8
replies
238
views
Piping samtools to R
R
NGS
bash
samtools
20 hours ago by
joe
▴ 470
1
vote
8
replies
336
views
0-based coordinates from samtools depth
samtools
coverage
depth
updated 3 days ago by
Pierre Lindenbaum
160k • written 3 days ago by
marco.barr
▴ 30
0
votes
8
replies
510
views
Fine-tuning NCBI taxid / taxidlist
BLAST
taxonomy
6 days ago by
theclubstyle
▴ 40
12
votes
7
replies
6.7k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 3 days ago by
dsull
★ 5.7k • written 2.6 years ago by
hamarillo
▴ 70
1
vote
7
replies
827
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 2 days ago by
Ram
43k • written 8 months ago by
Manuel Sokolov Ravasqueira
▴ 100
11
votes
7
replies
894
views
Shrink logFC values after edgeR
logFC
edgeR
updated 4 days ago by
Gordon Smyth
★ 6.9k • written 7 weeks ago by
arvind.1
▴ 10
3
votes
7
replies
523
views
Blast NCBI online using R
R
NCBI
BLAST
Rstudio
1 day ago by
Begonia_pavonina
▴ 140
2
votes
7
replies
594
views
Selecting query format for repeated calls to NCBI's API
NCBI
esummary
elink
API
efetch
updated 2 days ago by
GenoMax
140k • written 5 weeks ago by
LauferVA
4.1k
7
votes
7
replies
3.3k
views
How to perform normalization when converting ATAC bam file to bigwig file using deeptools for IGV visualization
bamCoverage
deeptools
bigwig
IGV
ATAC
updated 6 days ago by
sgv
• 0 • written 2.2 years ago by
sir.outman
▴ 40
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 3 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
0
votes
7
replies
310
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 16 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
6
votes
7
replies
622
views
cutadapt not trimming all adapters in PE Illumina sequencing
NGS
Illumina
cutadapt
5 days ago by
joe
▴ 470
2
votes
6
replies
452
views
Need help understanding core SNPs
SNPs
snippy
3 days ago by
ujichu
• 0
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 4 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
1
vote
6
replies
369
views
Coverage depth map of genome from multiple sample coverage bedgraphs?
bedops
bedmap
coverage
2 days ago by
Agastya
▴ 10
1
vote
6
replies
2.4k
views
Variant calling from multiple sequencing runs for a single samples
variant-calling
updated 2 days ago by
Ram
43k • written 6.9 years ago by
harish.nucl
• 0
8
votes
6
replies
385
views
Pangenome of plant
pangenome
plant
updated 22 hours ago by
talbots
• 0 • written 1 day ago by
analyst
▴ 10
0
votes
6
replies
406
views
Download Panther entry list
PANTHER
6 days ago by
Nicolas
• 0
1
vote
6
replies
461
views
Quest about the input data for PCA analysis
PCA
5 days ago by
tujuchuanli
▴ 100
2
votes
6
replies
3.3k
views
Base Quality of a reported variant in VCF
alignment
FASTQ
VCF
next-gen
Variant-Calling
updated 2 days ago by
Ram
43k • written 9.1 years ago by
VineethVenumadhavan
▴ 50
10
votes
6
replies
4.0k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 1 day ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
2
votes
5
replies
450
views
Searching for gene in multiple genomes
gene
genome
alignment
sequence
updated 5 days ago by
BioinfGuru
★ 1.6k • written 6 days ago by
Miya
• 0
3
votes
5
replies
376
views
Losing my mind with a VCF problem
vcf
bcftools
updated 5 days ago by
Michael
54k • written 5 days ago by
a.beggs
▴ 30
5
votes
5
replies
5.4k
views
beagle 4 exception: Duplicate marker
vcf
IBD
plink
beagle
updated 1 day ago by
Ram
43k • written 9.3 years ago by
galbarel
▴ 10
228 results • Page
1 of 5
Recent Votes
A: What Is The Sequencing 'Depth' ?
A: Read Duplicates
A: Read Duplicates
How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis?
Comment: Only one read per run - Trying to use CellRangerv7
Comment: Interproscan taking so much time
Answer: Interproscan taking so much time
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Devon Ryan
104k
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amitpande74
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160k
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Recent Replies
Answer: Can I have multiple active GDC download tokens?
by
Zhenyu Zhang
★ 1.1k
You can only have one active token at a time, but you can copy the same token as many times as you want and use them in different computers…
Comment: Parsing fasta file by coordinates
by
sorrymouse
▴ 120
Yes, thats correct. A lot of the responses are addressing problems other than the one I have - I don't want to cluster the sequences based …
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Not sure if I am missing something but you want 4 copies of the same sequence with a different fasta header?
Comment: Normalization strategies for comparing mapped reads across samples in RNA-seq
by
Ram
43k
> TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length. Also because TPM cannot be com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did run the `JoinLayers()` even then it is not working, here is the output before and after ```r DefaultAssay(combined1) <- 'RNA' com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I tried that too. It did not work.
Comment: (sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
by
GenoMax
140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
Comment: Issue with making local BLAST database
by
Begonia_pavonina
▴ 140
Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
Comment: Nanopore data filtering using fastp
by
GenoMax
140k
You can also use `reformat.sh` from [**BBMap suite**][1]. Look at sampling options. [1]: https://sourceforge.net/projects/bbmap/
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I was using it but the output file was too big pipe the output
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Share code and an example please.
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
Comment: Interproscan taking so much time
by
Mohamed Abderrahmane
▴ 10
Thank you for your reply. I have just executed the computation with parallelization as you mentioned, and I will observe the differences. H…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
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