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46 results • Page
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164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 22 hours ago by
Ram
43k • written 12.7 years ago by
Panos
★ 1.8k
3
votes
13
replies
445
views
Variant calling of GBS data
GBS
variants
BQSR
21 hours ago by
analyst
▴ 10
1
vote
12
replies
550
views
Nanopore data filtering using fastp
fastp
nanopore
23 hours ago by
emilydolivo97
• 0
1
vote
11
replies
316
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 21 hours ago by
GenoMax
140k • written 1 day ago by
Lila M
★ 1.2k
16
votes
10
replies
663
views
6 follow
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 1 hour ago by
Madelaine Gogol
5.3k • written 22 hours ago by
Ann
★ 2.4k
0
votes
9
replies
305
views
Low number of both surviving reads after trimming
trimmomatic
trimming
16 hours ago by
Jay
• 0
4
votes
9
replies
942
views
Error in openning FastQC
fastqc
igv
updated 16 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 20 hours ago by
Ram
43k • written 17 months ago by
Manav
• 0
1
vote
8
replies
3.2k
views
cutadapt error problem
next-gen
cutadapt
updated 22 hours ago by
Ram
43k • written 5.5 years ago by
amitpande74
▴ 20
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 22 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
0
votes
5
replies
145
views
Error running local blastn in R using system2
blastn
NCBI
R
just now by
Harrison
• 0
0
votes
5
replies
317
views
Parsing fasta file by coordinates
linux
fasta
updated 21 hours ago by
GenoMax
140k • written 3 days ago by
sorrymouse
▴ 120
2
votes
4
replies
338
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
21 hours ago by
Lissa Cruz Saavedra
• 0
0
votes
4
replies
219
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
15 hours ago by
BRENO
• 0
0
votes
3
replies
364
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
23 hours ago by
Nitin
• 0
2
votes
3
replies
2.1k
views
Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!
genome
next-gen
software-error
Assembly
updated 22 hours ago by
Ram
43k • written 4.0 years ago by
memy
▴ 20
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 22 hours ago by
Ram
43k • written 6.7 years ago by
namhaesly
• 0
2
votes
3
replies
125
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
updated 33 minutes ago by
GenoMax
140k • written 23 hours ago by
Mohamed Abderrahmane
▴ 10
0
votes
3
replies
83
views
Mapping ortholog human and mouse transcript
biomart
3 hours ago by
1769mkc
★ 1.2k
1
vote
2
replies
136
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 22 hours ago by
Ram
43k • written 1 day ago by
gdfsnkfns
• 0
2
votes
2
replies
136
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 23 hours ago by
dariober
14k • written 1 day ago by
Pumla
• 0
3
votes
2
replies
121
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
23 hours ago by
DYLAN NICO
• 0
0
votes
2
replies
132
views
ONT direct RNA sequencing
DRS
ONT
updated 20 hours ago by
Ram
43k • written 1 day ago by
Karina
• 0
1
vote
2
replies
143
views
Issue with making local BLAST database
R
mitochodrial
diatoms
blast
ncbi
updated 20 hours ago by
Ram
43k • written 1 day ago by
Begonia_pavonina
▴ 140
0
votes
2
replies
191
views
Can I have multiple active GDC download tokens?
TCGA
updated 23 hours ago by
Zhenyu Zhang
★ 1.1k • written 3 days ago by
mrk
• 0
1
vote
2
replies
224
views
DESeq2 and normalization
RNA-seq
normalization
DESeq2
5 hours ago by
JH
• 0
0
votes
2
replies
51
views
How do I get the gene annotations as a text file from a genebank file?
genebank
sequence-annotation
updated 28 minutes ago by
GenoMax
140k • written 5 hours ago by
eae6d2e7
• 0
0
votes
1
reply
101
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 16 hours ago by
Pierre Lindenbaum
160k • written 17 hours ago by
ekirsch
• 0
0
votes
1
reply
39
views
Alignment with new reference
alignment
updated 20 minutes ago by
GenoMax
140k • written 6 hours ago by
marco.barr
▴ 30
0
votes
1
reply
128
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 23 hours ago by
Ram
43k • written 1 day ago by
Picasa
▴ 640
1
vote
1
reply
109
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
updated 9 hours ago by
Soheil
▴ 100 • written 21 hours ago by
sithlordashley
• 0
0
votes
1
reply
485
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
updated 4 hours ago by
emilydolivo97
• 0 • written 2.1 years ago by
colindaven
6.3k
0
votes
1
reply
86
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
updated 3 hours ago by
BioinfGuru
★ 1.6k • written 15 hours ago by
Shicheng Guo
★ 9.4k
1
vote
1
reply
119
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
updated 3 hours ago by
Mensur Dlakic
★ 26k • written 5 hours ago by
Johannes W. Dietrich
• 0
0
votes
1
reply
104
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 20 hours ago by
Ram
43k • written 1 day ago by
Christian
• 0
0
votes
1
reply
131
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated 20 hours ago by
Lissa Cruz Saavedra
• 0 • written 1 day ago by
SAsciences
• 0
0
votes
1
reply
81
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 21 hours ago by
GenoMax
140k • written 22 hours ago by
David Tachiquín
• 0
0
votes
0
replies
72
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 23 hours ago by
Ram
43k • written 23 hours ago by
Tolga
▴ 20
0
votes
0
replies
86
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 23 hours ago by
Ram
43k • written 1 day ago by
udakshi
• 0
1
vote
0
replies
48
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
13 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
41
views
Convert to ENTREZGENE
maize
ENTREZGENE
12 hours ago by
sansan_96
▴ 50
0
votes
0
replies
32
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
9 hours ago by
analyst
▴ 10
0
votes
0
replies
69
views
News:
Online course: Reproducibility in Bioinformatics
Singularity
Version-Control
Docker
Containers
updated 19 hours ago by
Ram
43k • written 19 hours ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
35
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
9 hours ago by
pavithraashokkumar818
• 0
0
votes
0
replies
23
views
Plink merge errors.
merge
file
.bed
cygwin64
PLINK
updated 13 minutes ago by
GenoMax
140k • written 2 hours ago by
Dinmukhamed
• 0
0
votes
0
replies
60
views
News:
Online course: Analysis of Prokaryotic Pangenomes (Last call)
Prokaryotic
Bacterial-Genomics
Pangenomics
updated 19 hours ago by
Ram
43k • written 20 hours ago by
carlopecoraro2
★ 2.4k
46 results • Page
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Recent Votes
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
F*up Night style events for Bioinformatics ? Comment if you're interested!
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)
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Popular Question
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svlachavas
▴ 780
Teacher
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Pierre Lindenbaum
160k
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brian.fristensky
▴ 460
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Ann
★ 2.4k
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Recent Replies
Comment: Error running local blastn in R using system2
by
Harrison
• 0
Yes, in my actual script I use the whole path to nt_euk. I was just showing `C:/data/nt_euk` as shorthand for the full path. There are no s…
Comment: Error running local blastn in R using system2
by
Harrison
• 0
I am seeing `'cat' is not recognized as an internal or external command, operable program or batch file.`
Comment: Alignment with new reference
by
GenoMax
140k
> I'd like to realign my sequences to a reference that doesn't include > the base segment corresponding to the enzyme interval. How can I >…
Comment: How do I get the gene annotations as a text file from a genebank file?
by
GenoMax
140k
You will have to use a programming approach. BioPython is one option: https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
GenoMax
140k
> Is it because implementing multi-threading requires additional effort on their part Yes but in addition considerations here are importan…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Madelaine Gogol
5.3k
That sounds fun, and I've got some of these that I have told many people about (to keep them from making the same mistakes as me). I am pla…
Comment: Mapping ortholog human and mouse transcript
by
1769mkc
★ 1.2k
for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from g…
Comment: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of
by
Mensur Dlakic
★ 26k
Take it from someone who has hosted both a successful and a failed research topic: these deadlines are unrealistic. I am guessing you are p…
Answer: Tissue specific mRNA expression dataset in human and mouse
by
BioinfGuru
★ 1.6k
Awesome, years ago I wrote my thesis on the use of Tau to calculate tissue specificity, enjoy! The supplementary materials in the paper is…
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…
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