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235 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
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 18 hours ago by
Ram
43k • written 12.7 years ago by
Panos
★ 1.8k
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 22 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
5
votes
15
replies
4.8k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 6 days ago by
vague-barracuda-4686
• 0 • written 4.7 years ago by
Apprentice
▴ 160
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 1 day ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna
rRNA
metagenomics
updated 3 days ago by
Ram
43k • written 13.5 years ago by
toshnam
▴ 650
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
1
vote
13
replies
967
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 3 days ago by
lcj34
▴ 410 • written 9 days ago by
b.contreras.moreira
▴ 70
6
votes
13
replies
485
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
3 days ago by
Maverick
▴ 10
3
votes
13
replies
442
views
Variant calling of GBS data
GBS
variants
BQSR
17 hours ago by
analyst
▴ 10
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 2 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
1
vote
12
replies
547
views
Nanopore data filtering using fastp
fastp
nanopore
19 hours ago by
emilydolivo97
• 0
0
votes
12
replies
775
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
3 days ago by
biwdpang
• 0
3
votes
12
replies
640
views
Facing problem with extracting phenotypic data from GEO
WGCNA
GEO
2 days ago by
bioinfo_enthusiast
• 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
4
votes
11
replies
1.2k
views
Paired layout, but one fastq file
fastq
updated 1 day ago by
GenoMax
140k • written 12 months ago by
Andy
▴ 120
1
vote
11
replies
308
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 17 hours ago by
GenoMax
140k • written 23 hours ago by
Lila M
★ 1.2k
2
votes
11
replies
805
views
RNA seq aligner?
Alignment
4 days ago by
tesfaye
• 0
15
votes
10
replies
7.5k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 1 day ago by
Alex Reynolds
35k • written 8.2 years ago by
int11ap1
▴ 470
3
votes
10
replies
656
views
Intersect gene IDs list and GFF3 to get the annotation.
annotation
GFF
6 days ago by
Lissa Cruz Saavedra
• 0
2
votes
10
replies
730
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 20 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 16 hours ago by
Ram
43k • written 17 months ago by
Manav
• 0
15
votes
9
replies
621
views
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 14 hours ago by
Dave Carlson
★ 1.7k • written 18 hours ago by
Ann
★ 2.4k
0
votes
9
replies
292
views
Low number of both surviving reads after trimming
trimmomatic
trimming
12 hours ago by
Jay
• 0
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
2 days ago by
Zeng Jingyu
▴ 60
0
votes
9
replies
462
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 23 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
4
votes
9
replies
918
views
Error in openning FastQC
fastqc
igv
updated 12 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
4
votes
9
replies
671
views
Snakemake >= version 8 cluster configuration and SLURM job submission
parallelization
slurm
snakemake
cluster
updated 3 days ago by
Simon
▴ 10 • written 7 days ago by
Maxwell
▴ 20
2
votes
8
replies
263
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 470
1
vote
8
replies
342
views
0-based coordinates from samtools depth
samtools
coverage
depth
updated 3 days ago by
Pierre Lindenbaum
160k • written 4 days ago by
marco.barr
▴ 30
0
votes
8
replies
420
views
STAR aligner options
STAR
1 day ago by
theophile
• 0
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 18 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
1
vote
8
replies
3.2k
views
cutadapt error problem
next-gen
cutadapt
updated 18 hours ago by
Ram
43k • written 5.5 years ago by
amitpande74
▴ 20
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
1
vote
7
replies
831
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 5 days ago by
Gordon Smyth
★ 6.9k • written 8 weeks ago by
arvind.1
▴ 10
6
votes
7
replies
623
views
cutadapt not trimming all adapters in PE Illumina sequencing
NGS
Illumina
cutadapt
6 days ago by
joe
▴ 470
3
votes
7
replies
525
views
Blast NCBI online using R
R
NCBI
BLAST
Rstudio
2 days ago by
Begonia_pavonina
▴ 140
0
votes
7
replies
324
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 1 day ago by
GenoMax
140k • written 2 days ago by
Patadu94
• 0
12
votes
7
replies
6.7k
views
Forum:
Differences between SMART-seq2, SMART-seq3, and 10x
cell
smartseq
UMIs
single
10x
updated 4 days ago by
dsull
★ 5.7k • written 2.6 years ago by
hamarillo
▴ 70
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 4 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
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
2
votes
7
replies
599
views
Selecting query format for repeated calls to NCBI's API
NCBI
esummary
elink
API
efetch
updated 3 days ago by
GenoMax
140k • written 5 weeks ago by
LauferVA
4.1k
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 5 days ago by
marshelma
• 0 • written 4.5 years ago by
JJDollar
▴ 130
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
1
vote
6
replies
372
views
Coverage depth map of genome from multiple sample coverage bedgraphs?
bedops
bedmap
coverage
3 days ago by
Agastya
▴ 10
8
votes
6
replies
405
views
Pangenome of plant
pangenome
plant
updated 1 day ago by
talbots
• 0 • written 2 days ago by
analyst
▴ 10
2
votes
6
replies
453
views
Need help understanding core SNPs
SNPs
snippy
4 days ago by
ujichu
• 0
10
votes
6
replies
4.0k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 2 days ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
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
235 results • Page
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Recent Votes
Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Volume II
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: Mapping ortholog human and mouse transcript
by
BioinfGuru
★ 1.6k
That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host…
Comment: Nanopore multisample variant calling
by
emilydolivo97
• 0
hello @colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset
Comment: How do I get the gene annotations as a text file from a genebank file?
by
BioinfGuru
★ 1.6k
Can you upload or post a link to the genbank file please?
Comment: Mapping ortholog human and mouse transcript
by
manaswwm
▴ 490
I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
by
JH
• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
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