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55 results • Page
1 of 2
Sort: Votes
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Views
Votes
Replies
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 13 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 17 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
15
votes
9
replies
593
views
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 9 hours ago by
Dave Carlson
★ 1.7k • written 13 hours ago by
Ann
★ 2.4k
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 13 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
4
votes
9
replies
893
views
Error in openning FastQC
fastqc
igv
updated 7 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
3
votes
13
replies
440
views
Variant calling of GBS data
GBS
variants
BQSR
12 hours ago by
analyst
▴ 10
3
votes
2
replies
96
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
14 hours ago by
DYLAN NICO
• 0
2
votes
2
replies
119
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 14 hours ago by
dariober
14k • written 19 hours ago by
Pumla
• 0
2
votes
3
replies
2.1k
views
Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!
genome
next-gen
software-error
Assembly
updated 13 hours ago by
Ram
43k • written 4.0 years ago by
memy
▴ 20
2
votes
2
replies
137
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 19 hours ago by
dthorbur
★ 1.7k • written 20 hours ago by
Mohamed Abderrahmane
▴ 10
2
votes
10
replies
724
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 15 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
2
votes
4
replies
323
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
12 hours ago by
Lissa Cruz Saavedra
• 0
1
vote
8
replies
3.2k
views
cutadapt error problem
next-gen
cutadapt
updated 13 hours ago by
Ram
43k • written 5.5 years ago by
amitpande74
▴ 20
1
vote
2
replies
122
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 13 hours ago by
Ram
43k • written 18 hours ago by
gdfsnkfns
• 0
1
vote
1
reply
285
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
18 hours ago by
Pierre Lindenbaum
160k
1
vote
0
replies
24
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
4 hours ago by
Shicheng Guo
★ 9.4k
1
vote
2
replies
133
views
Issue with making local BLAST database
R
mitochodrial
diatoms
blast
ncbi
updated 11 hours ago by
Ram
43k • written 17 hours ago by
Begonia_pavonina
▴ 140
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 11 hours ago by
Ram
43k • written 17 months ago by
Manav
• 0
1
vote
12
replies
543
views
Nanopore data filtering using fastp
fastp
nanopore
14 hours ago by
emilydolivo97
• 0
1
vote
11
replies
302
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 12 hours ago by
GenoMax
140k • written 18 hours ago by
Lila M
★ 1.2k
0
votes
1
reply
66
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 12 hours ago by
GenoMax
140k • written 13 hours ago by
David Tachiquín
• 0
0
votes
1
reply
117
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated 12 hours ago by
Lissa Cruz Saavedra
• 0 • written 1 day ago by
SAsciences
• 0
0
votes
2
replies
120
views
ONT direct RNA sequencing
DRS
ONT
updated 11 hours ago by
Ram
43k • written 18 hours ago by
Karina
• 0
0
votes
1
reply
92
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 11 hours ago by
Ram
43k • written 19 hours ago by
Christian
• 0
0
votes
0
replies
55
views
News:
Online course: Reproducibility in Bioinformatics
Singularity
Version-Control
Docker
Containers
updated 10 hours ago by
Ram
43k • written 10 hours ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
49
views
News:
Online course: Analysis of Prokaryotic Pangenomes (Last call)
Prokaryotic
Bacterial-Genomics
Pangenomics
updated 10 hours ago by
Ram
43k • written 11 hours ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
74
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 7 hours ago by
Pierre Lindenbaum
160k • written 8 hours ago by
ekirsch
• 0
0
votes
9
replies
273
views
Low number of both surviving reads after trimming
trimmomatic
trimming
7 hours ago by
Jay
• 0
0
votes
2
replies
107
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 7 hours ago by
Mensur Dlakic
★ 26k • written 10 hours ago by
Harrison
• 0
0
votes
4
replies
172
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
6 hours ago by
BRENO
• 0
0
votes
0
replies
29
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
6 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
18
views
Convert to ENTREZGENE
maize
ENTREZGENE
3 hours ago by
sansan_96
▴ 50
0
votes
0
replies
9
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
40 minutes ago by
analyst
▴ 10
0
votes
1
reply
64
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
updated 20 minutes ago by
Soheil
▴ 90 • written 12 hours ago by
sithlordashley
• 0
0
votes
0
replies
81
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
21 hours ago by
liuyibin2005
• 0
0
votes
0
replies
3
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
10 minutes ago by
pavithraashokkumar818
• 0
0
votes
0
replies
68
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
20 hours ago by
blur
▴ 280
0
votes
8
replies
419
views
STAR aligner options
STAR
20 hours ago by
theophile
• 0
0
votes
0
replies
72
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
20 hours ago by
Broccoli
• 0
0
votes
3
replies
223
views
convert cds to seurat object
R
monocle3
seurat
updated 18 hours ago by
edoardofilippi1998
• 0 • written 1 day ago by
sooni
▴ 20
0
votes
4
replies
244
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
18 hours ago by
rohitsatyam102
▴ 840
0
votes
9
replies
460
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 18 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
0
votes
0
replies
91
views
Training
chip-seq
ScATAC-seq
17 hours ago by
Manhezz
• 0
0
votes
0
replies
65
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 15 hours ago by
Ram
43k • written 21 hours ago by
M'zelle
• 0
0
votes
5
replies
236
views
calculate mismatch rate from VCF file
mismatch-rate
VCF
updated 15 hours ago by
Ram
43k • written 1 day ago by
Dora
▴ 10
0
votes
1
reply
90
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 15 hours ago by
Ram
43k • written 15 hours ago by
chiditatawmbi
• 0
0
votes
0
replies
55
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
14 hours ago by
alenew.am
• 0
0
votes
0
replies
60
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 14 hours ago by
Ram
43k • written 14 hours ago by
Tolga
▴ 20
0
votes
1
reply
113
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 14 hours ago by
Ram
43k • written 16 hours ago by
Picasa
▴ 640
0
votes
3
replies
313
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
14 hours ago by
Nitin
• 0
55 results • Page
1 of 2
Recent Votes
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!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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160k
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Recent Replies
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…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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