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116,015 results • Page
1 of 2321
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0
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ONT direct RNA sequencing
gz
DRS
ONT
gunzip
gzip
updated 15 minutes ago by
joe
▴ 470 • written 4 hours ago by
Karina
• 0
0
votes
0
replies
8
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
27 minutes ago by
Mohamed Abderrahmane
▴ 10
2
votes
2
replies
10
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
just now by
DYLAN NICO
• 0
0
votes
2
replies
136
views
Can I have multiple active GDC download tokens?
TCGA
updated 34 minutes ago by
Zhenyu Zhang
★ 1.1k • written 2 days ago by
mrk
• 0
0
votes
0
replies
14
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 54 minutes ago by
Ram
43k • written 59 minutes ago by
Tolga
▴ 20
0
votes
0
replies
13
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
59 minutes ago by
alenew.am
• 0
0
votes
3
replies
170
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
40 minutes ago by
Nitin
• 0
0
votes
1
reply
24
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 1 hour ago by
Ram
43k • written 1 hour ago by
chiditatawmbi
• 0
0
votes
1
reply
43
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 48 minutes ago by
Ram
43k • written 2 hours ago by
Picasa
▴ 640
0
votes
0
replies
38
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 30 minutes ago by
Ram
43k • written 3 hours ago by
udakshi
• 0
0
votes
0
replies
49
views
Training
chip-seq
ScATAC-seq
3 hours ago by
Manhezz
• 0
1
vote
2
replies
63
views
Issue with making local BLAST database
database
mitochodrial
diatoms
blast
ncbi
1 hour ago by
Begonia_pavonina
▴ 140
1
vote
1
reply
251
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
4 hours ago by
Pierre Lindenbaum
160k
793
votes
167
replies
139k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.6k • written 7.3 years ago by
Istvan Albert
100k
1
vote
10
replies
174
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
10 minutes ago by
Lila M
★ 1.2k
2
votes
2
replies
63
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated just now by
dariober
14k • written 5 hours ago by
Pumla
• 0
0
votes
1
reply
65
views
Merging featureCounts output for different species
featureCount
RNAseq
updated 5 hours ago by
andrebolerbarros
• 0 • written 6 hours ago by
Christian
• 0
2
votes
2
replies
88
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 5 hours ago by
dthorbur
★ 1.7k • written 6 hours ago by
Mohamed Abderrahmane
▴ 10
0
votes
0
replies
45
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
6 hours ago by
Broccoli
• 0
0
votes
0
replies
44
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
6 hours ago by
blur
▴ 280
0
votes
0
replies
53
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
7 hours ago by
liuyibin2005
• 0
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 3 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
0
votes
0
replies
41
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 1 hour ago by
Ram
43k • written 7 hours ago by
M'zelle
• 0
0
votes
5
replies
182
views
calculate mismatch rate from VCF file
mismatch-rate
VCF
updated 1 hour ago by
Ram
43k • written 13 hours ago by
Dora
▴ 10
2
votes
3
replies
263
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
updated 7 hours ago by
colindaven
6.3k • written 2 days ago by
Lissa Cruz Saavedra
• 0
0
votes
0
replies
62
views
In scRNA, How should I set QC standards?
scRNA
QC
10 hours ago by
mnx0723
• 0
0
votes
0
replies
52
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated 1 hour ago by
Ram
43k • written 11 hours ago by
SAsciences
• 0
0
votes
2
replies
225
views
Error occurs when migrate-n software performs "make mpis"
migrate-n
12 hours ago by
lingxue
• 0
0
votes
0
replies
61
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
13 hours ago by
Chris
▴ 260
2
votes
10
replies
698
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 1 hour ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
3
votes
2
replies
267
views
FDR and Bonferroni
FDR
Bonferroni
updated 13 hours ago by
joe
▴ 470 • written 2 days ago by
song
• 0
0
votes
1
reply
471
views
Which fasta files are assembled transcripts IDBA_tran assembler ?
RNA-Seq
Assembly
updated 16 hours ago by
weidonglu
• 0 • written 3.8 years ago by
sunnykevin97
▴ 980
0
votes
0
replies
77
views
doing some ontology enrichment analysis
GO
16 hours ago by
aleksk779
• 0
2
votes
1
reply
170
views
Choosing an FC Threshold
statistics
rna-seq
updated 16 hours ago by
Gordon Smyth
★ 6.9k • written 1 day ago by
Netanel
• 0
0
votes
1
reply
109
views
Converting AutoDock-Vina PDBQTs to PDB files
Docking
AutoDock
Vina
PDBQT
PDB
updated 19 hours ago by
Mensur Dlakic
★ 26k • written 1 day ago by
Ricard
• 0
0
votes
2
replies
147
views
novel and know mir156 and mir172
a
updated 15 hours ago by
gayachit
▴ 200 • written 19 hours ago by
Fadmo
• 0
0
votes
1
reply
96
views
Update R in Posit Workbench
R
Posit
updated 20 hours ago by
Ram
43k • written 20 hours ago by
Nitin
• 0
2
votes
8
replies
240
views
Piping samtools to R
R
NGS
bash
samtools
20 hours ago by
joe
▴ 470
8
votes
6
replies
386
views
Pangenome of plant
pangenome
plant
updated 22 hours ago by
talbots
• 0 • written 2 days ago by
analyst
▴ 10
1
vote
2
replies
175
views
vg call is time consuming
vg
22 hours ago by
Maxine
▴ 40
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 22 hours ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
0
votes
8
replies
406
views
STAR aligner options
STAR
6 hours ago by
theophile
• 0
2
votes
3
replies
506
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 23 hours ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
0
votes
2
replies
292
views
How to obtain Node/ Edge information from a Reactome Pathway
R
API
pathways
reactome
databases
updated 22 hours ago by
GenoMax
140k • written 4 weeks ago by
K.patel5
▴ 140
0
votes
2
replies
156
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
18 hours ago by
Ankit
▴ 500
0
votes
1
reply
103
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 22 hours ago by
Yogi
▴ 70 • written 1 day ago by
Ronin
• 0
0
votes
0
replies
80
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 22 hours ago by
Ram
43k • written 1 day ago by
r.shiasi3897
▴ 10
0
votes
0
replies
80
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
0
votes
1
reply
119
views
How can I remove duplicate SNP?
plink
updated 1 day ago by
iraun
6.2k • written 1 day ago by
Zhennan
• 0
0
votes
1
reply
129
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 22 hours ago by
Ram
43k • written 1 day ago by
Hajar
• 0
116,015 results • Page
1 of 2321
Recent Votes
Comment: Gene reads all zero for each sample
A: What Is The Sequencing 'Depth' ?
A: Read Duplicates
A: Read Duplicates
How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis?
Comment: Only one read per run - Trying to use CellRangerv7
Comment: Interproscan taking so much time
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Recent Replies
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
They are +ve and -ve strands, but identical two by two ... I can filter that out later on. This is probably a very naive question, but what…
Comment: Gene reads all zero for each sample
by
ATpoint
81k
Do I understand correctly that you have one gene you are interested in, but all counts are zero, right? If so, first thing could be to use …
Answer: ONT direct RNA sequencing
by
joe
▴ 470
You should use `cat` on .gz files, part of the magic of .gz ...I guess if you use `zcat` they are unzipped and this is why you get the erro…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you !!
Answer: Can I have multiple active GDC download tokens?
by
Zhenyu Zhang
★ 1.1k
You can only have one active token at a time, but you can copy the same token as many times as you want and use them in different computers…
Comment: Parsing fasta file by coordinates
by
sorrymouse
▴ 120
Yes, thats correct. A lot of the responses are addressing problems other than the one I have - I don't want to cluster the sequences based …
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Not sure if I am missing something but you want 4 copies of the same sequence with a different fasta header?
Comment: Normalization strategies for comparing mapped reads across samples in RNA-seq
by
Ram
43k
> TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length. Also because TPM cannot be com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did run the `JoinLayers()` even then it is not working, here is the output before and after ```r DefaultAssay(combined1) <- 'RNA' com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I tried that too. It did not work.
Comment: (sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
by
GenoMax
140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
Comment: Issue with making local BLAST database
by
Begonia_pavonina
▴ 140
Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
Comment: Nanopore data filtering using fastp
by
GenoMax
140k
You can also use `reformat.sh` from [**BBMap suite**][1]. Look at sampling options. [1]: https://sourceforge.net/projects/bbmap/
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I was using it but the output file was too big pipe the output
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