Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : today
all time
today
this week
this month
this year
56 results • Page
1 of 2
Sort: Votes
Rank
Views
Votes
Replies
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 15 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 19 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
15
votes
9
replies
600
views
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 11 hours ago by
Dave Carlson
★ 1.7k • written 15 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 15 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
4
votes
9
replies
896
views
Error in openning FastQC
fastqc
igv
updated 9 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
3
votes
13
replies
442
views
Variant calling of GBS data
GBS
variants
BQSR
13 hours ago by
analyst
▴ 10
3
votes
2
replies
97
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
15 hours ago by
DYLAN NICO
• 0
2
votes
4
replies
325
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
13 hours ago by
Lissa Cruz Saavedra
• 0
2
votes
2
replies
122
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 15 hours ago by
dariober
14k • written 20 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 15 hours ago by
Ram
43k • written 4.0 years ago by
memy
▴ 20
2
votes
2
replies
139
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 21 hours ago by
dthorbur
★ 1.7k • written 21 hours ago by
Mohamed Abderrahmane
▴ 10
2
votes
10
replies
726
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 17 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
1
vote
2
replies
123
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 15 hours ago by
Ram
43k • written 19 hours ago by
gdfsnkfns
• 0
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 13 hours ago by
Ram
43k • written 17 months ago by
Manav
• 0
1
vote
0
replies
27
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
6 hours ago by
Shicheng Guo
★ 9.4k
1
vote
11
replies
305
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 14 hours ago by
GenoMax
140k • written 20 hours ago by
Lila M
★ 1.2k
1
vote
12
replies
544
views
Nanopore data filtering using fastp
fastp
nanopore
15 hours ago by
emilydolivo97
• 0
1
vote
2
replies
135
views
Issue with making local BLAST database
R
mitochodrial
diatoms
blast
ncbi
updated 12 hours ago by
Ram
43k • written 19 hours ago by
Begonia_pavonina
▴ 140
1
vote
1
reply
288
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
19 hours ago by
Pierre Lindenbaum
160k
1
vote
8
replies
3.2k
views
cutadapt error problem
next-gen
cutadapt
updated 15 hours ago by
Ram
43k • written 5.5 years ago by
amitpande74
▴ 20
0
votes
1
reply
68
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 13 hours ago by
GenoMax
140k • written 14 hours ago by
David Tachiquín
• 0
0
votes
1
reply
120
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated 13 hours ago by
Lissa Cruz Saavedra
• 0 • written 1 day ago by
SAsciences
• 0
0
votes
2
replies
122
views
ONT direct RNA sequencing
DRS
ONT
updated 13 hours ago by
Ram
43k • written 19 hours ago by
Karina
• 0
0
votes
1
reply
94
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 12 hours ago by
Ram
43k • written 21 hours ago by
Christian
• 0
0
votes
0
replies
57
views
News:
Online course: Reproducibility in Bioinformatics
Singularity
Version-Control
Docker
Containers
updated 11 hours ago by
Ram
43k • written 12 hours ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
51
views
News:
Online course: Analysis of Prokaryotic Pangenomes (Last call)
Prokaryotic
Bacterial-Genomics
Pangenomics
updated 11 hours ago by
Ram
43k • written 12 hours ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
80
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 9 hours ago by
Pierre Lindenbaum
160k • written 9 hours ago by
ekirsch
• 0
0
votes
9
replies
276
views
Low number of both surviving reads after trimming
trimmomatic
trimming
8 hours ago by
Jay
• 0
0
votes
2
replies
109
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 8 hours ago by
Mensur Dlakic
★ 26k • written 11 hours ago by
Harrison
• 0
0
votes
4
replies
180
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
8 hours ago by
BRENO
• 0
0
votes
0
replies
32
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
7 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
22
views
Convert to ENTREZGENE
maize
ENTREZGENE
5 hours ago by
sansan_96
▴ 50
0
votes
0
replies
13
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
2 hours ago by
analyst
▴ 10
0
votes
1
reply
71
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
updated 1 hour ago by
Soheil
▴ 90 • written 13 hours ago by
sithlordashley
• 0
0
votes
0
replies
10
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
1 hour ago by
pavithraashokkumar818
• 0
0
votes
0
replies
83
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
22 hours ago by
liuyibin2005
• 0
0
votes
0
replies
4
views
Mapping ortholog human and mouse transcript
biomart
20 minutes ago by
1769mkc
★ 1.2k
0
votes
0
replies
70
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
21 hours ago by
blur
▴ 280
0
votes
8
replies
419
views
STAR aligner options
STAR
21 hours ago by
theophile
• 0
0
votes
0
replies
74
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
21 hours ago by
Broccoli
• 0
0
votes
3
replies
223
views
convert cds to seurat object
R
monocle3
seurat
updated 20 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
19 hours ago by
rohitsatyam102
▴ 840
0
votes
9
replies
461
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 19 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
0
votes
0
replies
93
views
Training
chip-seq
ScATAC-seq
19 hours ago by
Manhezz
• 0
0
votes
0
replies
66
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 16 hours ago by
Ram
43k • written 22 hours ago by
M'zelle
• 0
0
votes
5
replies
238
views
calculate mismatch rate from VCF file
mismatch-rate
VCF
updated 17 hours ago by
Ram
43k • written 1 day ago by
Dora
▴ 10
0
votes
1
reply
92
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 16 hours ago by
Ram
43k • written 17 hours ago by
chiditatawmbi
• 0
0
votes
0
replies
57
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
16 hours ago by
alenew.am
• 0
0
votes
0
replies
62
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 16 hours ago by
Ram
43k • written 16 hours ago by
Tolga
▴ 20
0
votes
1
reply
114
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 16 hours ago by
Ram
43k • written 17 hours ago by
Picasa
▴ 640
56 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!
Recent Locations •
All
South Korea,
2 minutes ago
united state,
3 minutes ago
Italy,
4 minutes ago
Singapore,
7 minutes ago
Machhagan,
11 minutes ago
Bologna,
11 minutes ago
Chile,
11 minutes ago
Recent Awards •
All
Teacher
to
Pierre Lindenbaum
160k
Popular Question
to
brian.fristensky
▴ 460
Popular Question
to
Ann
★ 2.4k
Commentator
to
GenoMax
140k
Commentator
to
Devon Ryan
104k
Popular Question
to
amitpande74
▴ 20
Popular Question
to
beacamara
• 0
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…
Traffic: 2194 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6