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56 results • Page
1 of 2
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Votes
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164
votes
70
replies
60k
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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
15
votes
9
replies
625
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
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
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
3
votes
13
replies
442
views
Variant calling of GBS data
GBS
variants
BQSR
17 hours ago by
analyst
▴ 10
3
votes
2
replies
113
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
19 hours ago by
DYLAN NICO
• 0
2
votes
3
replies
2.1k
views
Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!
genome
next-gen
software-error
Assembly
updated 18 hours ago by
Ram
43k • written 4.0 years ago by
memy
▴ 20
2
votes
4
replies
331
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
17 hours 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
2
votes
2
replies
128
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 19 hours ago by
dariober
14k • written 1 day ago by
Pumla
• 0
1
vote
2
replies
138
views
Issue with making local BLAST database
R
mitochodrial
diatoms
blast
ncbi
updated 16 hours ago by
Ram
43k • written 22 hours ago by
Begonia_pavonina
▴ 140
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
1
vote
2
replies
127
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 18 hours ago by
Ram
43k • written 23 hours ago by
gdfsnkfns
• 0
1
vote
1
reply
291
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
23 hours ago by
Pierre Lindenbaum
160k
1
vote
0
replies
39
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
10 hours ago by
Shicheng Guo
★ 9.4k
1
vote
11
replies
309
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
1
vote
12
replies
547
views
Nanopore data filtering using fastp
fastp
nanopore
19 hours ago by
emilydolivo97
• 0
1
vote
2
replies
109
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
2 hours ago by
Mohamed Abderrahmane
▴ 10
1
vote
2
replies
221
views
DESeq2 and normalization
RNA-seq
normalization
DESeq2
1 hour ago by
JH
• 0
1
vote
0
replies
42
views
News:
Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Vol…
systems_biology
endocrinology
machine_learning
ML
mathematical_modelling
1 hour ago by
Johannes W. Dietrich
• 0
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
0
votes
9
replies
293
views
Low number of both surviving reads after trimming
trimmomatic
trimming
12 hours ago by
Jay
• 0
0
votes
2
replies
124
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 12 hours ago by
Mensur Dlakic
★ 26k • written 15 hours ago by
Harrison
• 0
0
votes
4
replies
203
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
11 hours ago by
BRENO
• 0
0
votes
0
replies
41
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
11 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
32
views
Convert to ENTREZGENE
maize
ENTREZGENE
8 hours ago by
sansan_96
▴ 50
0
votes
0
replies
20
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
5 hours ago by
analyst
▴ 10
0
votes
1
reply
95
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
updated 5 hours ago by
Soheil
▴ 90 • written 17 hours ago by
sithlordashley
• 0
0
votes
0
replies
25
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
5 hours ago by
pavithraashokkumar818
• 0
0
votes
0
replies
22
views
Alignment with new reference
alignment
2 hours ago by
marco.barr
▴ 30
0
votes
1
reply
21
views
How do I get the gene annotations as a text file from a genebank file?
genebank
sequence-annotation
updated 40 minutes ago by
BioinfGuru
★ 1.6k • written 1 hour ago by
eae6d2e7
• 0
0
votes
1
reply
475
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
updated 30 minutes ago by
emilydolivo97
• 0 • written 2.1 years ago by
colindaven
6.3k
0
votes
3
replies
223
views
convert cds to seurat object
R
monocle3
seurat
updated 23 hours ago by
edoardofilippi1998
• 0 • written 2 days ago by
sooni
▴ 20
0
votes
2
replies
41
views
Mapping ortholog human and mouse transcript
biomart
updated 10 minutes ago by
BioinfGuru
★ 1.6k • written 3 hours ago by
1769mkc
★ 1.2k
0
votes
4
replies
246
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
23 hours ago by
rohitsatyam102
▴ 840
0
votes
9
replies
462
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 23 hours ago by
GenoMax
140k • written 7 days ago by
dzisis1986
▴ 70
0
votes
0
replies
99
views
Training
chip-seq
ScATAC-seq
22 hours ago by
Manhezz
• 0
0
votes
0
replies
73
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 20 hours ago by
Ram
43k • written 1 day ago by
M'zelle
• 0
0
votes
5
replies
246
views
calculate mismatch rate from VCF file
mismatch-rate
VCF
updated 20 hours ago by
Ram
43k • written 1 day ago by
Dora
▴ 10
0
votes
1
reply
99
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 20 hours ago by
Ram
43k • written 20 hours ago by
chiditatawmbi
• 0
0
votes
0
replies
61
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
20 hours ago by
alenew.am
• 0
0
votes
0
replies
66
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 19 hours ago by
Ram
43k • written 20 hours ago by
Tolga
▴ 20
0
votes
1
reply
120
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 19 hours ago by
Ram
43k • written 21 hours ago by
Picasa
▴ 640
0
votes
3
replies
357
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
19 hours ago by
Nitin
• 0
0
votes
2
replies
184
views
Can I have multiple active GDC download tokens?
TCGA
updated 19 hours ago by
Zhenyu Zhang
★ 1.1k • written 3 days ago by
mrk
• 0
0
votes
0
replies
81
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 19 hours ago by
Ram
43k • written 22 hours ago by
udakshi
• 0
0
votes
3
replies
3.0k
views
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
R
next-gen-sequencing
absolute
updated 18 hours ago by
Ram
43k • written 6.7 years ago by
namhaesly
• 0
0
votes
5
replies
317
views
Parsing fasta file by coordinates
linux
fasta
updated 18 hours ago by
GenoMax
140k • written 3 days ago by
sorrymouse
▴ 120
0
votes
1
reply
75
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 17 hours ago by
GenoMax
140k • written 18 hours ago by
David Tachiquín
• 0
56 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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Answer: 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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