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57 results • Page
1 of 2
Sort: Views
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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 16 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 20 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 16 hours ago by
Ram
43k • written 9.8 years ago by
Kizuna
▴ 870
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 14 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 16 hours ago by
Ram
43k • written 5.5 years ago by
amitpande74
▴ 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 16 hours ago by
Ram
43k • written 6.7 years ago by
namhaesly
• 0
2
votes
3
replies
2.1k
views
Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!
genome
next-gen
software-error
Assembly
updated 16 hours ago by
Ram
43k • written 4.0 years ago by
memy
▴ 20
4
votes
9
replies
906
views
Error in openning FastQC
fastqc
igv
updated 10 hours ago by
GenoMax
140k • written 7 months ago by
huynhthienphai
• 0
2
votes
10
replies
727
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 18 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
15
votes
9
replies
612
views
Forum:
F*up Night style events for Bioinformatics ? Comment if you're interested!
mistakes
updated 12 hours ago by
Dave Carlson
★ 1.7k • written 16 hours ago by
Ann
★ 2.4k
1
vote
12
replies
546
views
Nanopore data filtering using fastp
fastp
nanopore
17 hours ago by
emilydolivo97
• 0
0
votes
9
replies
461
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 20 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
3
votes
13
replies
442
views
Variant calling of GBS data
GBS
variants
BQSR
15 hours ago by
analyst
▴ 10
0
votes
8
replies
419
views
STAR aligner options
STAR
22 hours ago by
theophile
• 0
0
votes
3
replies
345
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
17 hours ago by
Nitin
• 0
2
votes
4
replies
327
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
14 hours ago by
Lissa Cruz Saavedra
• 0
0
votes
5
replies
317
views
Parsing fasta file by coordinates
linux
fasta
updated 15 hours ago by
GenoMax
140k • written 3 days ago by
sorrymouse
▴ 120
1
vote
11
replies
307
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 15 hours ago by
GenoMax
140k • written 21 hours ago by
Lila M
★ 1.2k
1
vote
1
reply
289
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
20 hours ago by
Pierre Lindenbaum
160k
0
votes
9
replies
285
views
Low number of both surviving reads after trimming
trimmomatic
trimming
10 hours ago by
Jay
• 0
0
votes
4
replies
244
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
21 hours ago by
rohitsatyam102
▴ 840
0
votes
5
replies
240
views
calculate mismatch rate from VCF file
mismatch-rate
VCF
updated 18 hours ago by
Ram
43k • written 1 day ago by
Dora
▴ 10
0
votes
3
replies
223
views
convert cds to seurat object
R
monocle3
seurat
updated 21 hours ago by
edoardofilippi1998
• 0 • written 1 day ago by
sooni
▴ 20
0
votes
4
replies
195
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
9 hours ago by
BRENO
• 0
0
votes
2
replies
182
views
Can I have multiple active GDC download tokens?
TCGA
updated 17 hours ago by
Zhenyu Zhang
★ 1.1k • written 3 days ago by
mrk
• 0
2
votes
2
replies
143
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 22 hours ago by
dthorbur
★ 1.7k • written 22 hours ago by
Mohamed Abderrahmane
▴ 10
1
vote
2
replies
136
views
Issue with making local BLAST database
R
mitochodrial
diatoms
blast
ncbi
updated 14 hours ago by
Ram
43k • written 20 hours ago by
Begonia_pavonina
▴ 140
2
votes
2
replies
126
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 16 hours ago by
dariober
14k • written 22 hours ago by
Pumla
• 0
1
vote
2
replies
125
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 16 hours ago by
Ram
43k • written 21 hours ago by
gdfsnkfns
• 0
0
votes
2
replies
124
views
ONT direct RNA sequencing
DRS
ONT
updated 14 hours ago by
Ram
43k • written 21 hours ago by
Karina
• 0
0
votes
1
reply
121
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated 14 hours ago by
Lissa Cruz Saavedra
• 0 • written 1 day ago by
SAsciences
• 0
0
votes
2
replies
116
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 9 hours ago by
Mensur Dlakic
★ 26k • written 12 hours ago by
Harrison
• 0
0
votes
1
reply
117
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 17 hours ago by
Ram
43k • written 19 hours ago by
Picasa
▴ 640
3
votes
2
replies
106
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
16 hours ago by
DYLAN NICO
• 0
0
votes
0
replies
96
views
Training
chip-seq
ScATAC-seq
20 hours ago by
Manhezz
• 0
0
votes
1
reply
96
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 14 hours ago by
Ram
43k • written 22 hours ago by
Christian
• 0
0
votes
1
reply
95
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 18 hours ago by
Ram
43k • written 18 hours ago by
chiditatawmbi
• 0
1
vote
1
reply
88
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
updated 15 hours ago by
GenoMax
140k • written 17 hours ago by
Mohamed Abderrahmane
▴ 10
0
votes
1
reply
85
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 10 hours ago by
Pierre Lindenbaum
160k • written 11 hours ago by
ekirsch
• 0
0
votes
0
replies
84
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
23 hours ago by
liuyibin2005
• 0
0
votes
1
reply
81
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
updated 3 hours ago by
Soheil
▴ 90 • written 14 hours ago by
sithlordashley
• 0
0
votes
0
replies
77
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 17 hours ago by
Ram
43k • written 20 hours ago by
udakshi
• 0
0
votes
0
replies
75
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
22 hours ago by
Broccoli
• 0
0
votes
1
reply
72
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 15 hours ago by
GenoMax
140k • written 15 hours ago by
David Tachiquín
• 0
0
votes
0
replies
71
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
23 hours ago by
blur
▴ 280
0
votes
0
replies
69
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 18 hours ago by
Ram
43k • written 1 day ago by
M'zelle
• 0
0
votes
0
replies
64
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 17 hours ago by
Ram
43k • written 17 hours ago by
Tolga
▴ 20
0
votes
0
replies
59
views
News:
Online course: Reproducibility in Bioinformatics
Singularity
Version-Control
Docker
Containers
updated 13 hours ago by
Ram
43k • written 13 hours ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
58
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
17 hours ago by
alenew.am
• 0
0
votes
0
replies
52
views
News:
Online course: Analysis of Prokaryotic Pangenomes (Last call)
Prokaryotic
Bacterial-Genomics
Pangenomics
updated 13 hours ago by
Ram
43k • written 14 hours ago by
carlopecoraro2
★ 2.4k
57 results • Page
1 of 2
Recent Votes
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!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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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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