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33 results • Page
1 of 1
Sort: Views
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Views
Votes
Replies
2
votes
10
replies
695
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 10 minutes ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
0
votes
9
replies
443
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 2 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
1
vote
11
replies
426
views
Nanopore data filtering using fastp
fastp
nanopore
35 minutes ago by
emilydolivo97
• 0
0
votes
8
replies
402
views
STAR aligner options
STAR
4 hours ago by
theophile
• 0
0
votes
7
replies
309
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 15 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
4
replies
261
views
Parsing fasta file by coordinates
linux
fasta
updated 3 hours ago by
Joe
21k • written 2 days ago by
sorrymouse
▴ 120
0
votes
4
replies
235
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
3 hours ago by
rohitsatyam102
▴ 840
2
votes
8
replies
233
views
Piping samtools to R
R
NGS
bash
samtools
19 hours ago by
joe
▴ 470
2
votes
2
replies
205
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 23 hours ago by
Pierre Lindenbaum
160k • written 1 day ago by
fred.s.kremer
▴ 110
0
votes
2
replies
154
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
16 hours ago by
Ankit
▴ 500
0
votes
2
replies
149
views
Error with goodSamplesGenes()
R
WGCNA
21 hours ago by
bioinfo_enthusiast
• 0
0
votes
2
replies
145
views
novel and know mir156 and mir172
a
updated 14 hours ago by
gayachit
▴ 200 • written 18 hours ago by
Fadmo
• 0
1
vote
8
replies
125
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
1 hour ago by
Lila M
★ 1.2k
0
votes
1
reply
128
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 21 hours ago by
Ram
43k • written 1 day ago by
Hajar
• 0
0
votes
1
reply
116
views
How can I remove duplicate SNP?
plink
updated 23 hours ago by
iraun
6.2k • written 23 hours ago by
Zhennan
• 0
0
votes
1
reply
102
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 21 hours ago by
Yogi
▴ 70 • written 22 hours ago by
Ronin
• 0
0
votes
0
replies
78
views
Number of pathway result from GSVA
GSVA
23 hours ago by
Chris
▴ 260
0
votes
0
replies
79
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 21 hours ago by
Ram
43k • written 23 hours ago by
r.shiasi3897
▴ 10
0
votes
0
replies
75
views
doing some ontology enrichment analysis
GO
15 hours ago by
aleksk779
• 0
0
votes
1
reply
62
views
Merging featureCounts output for different species
featureCount
RNAseq
updated 4 hours ago by
andrebolerbarros
• 0 • written 4 hours ago by
Christian
• 0
0
votes
0
replies
60
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
12 hours ago by
Chris
▴ 260
0
votes
0
replies
59
views
In scRNA, How should I set QC standards?
scRNA
QC
8 hours ago by
mnx0723
• 0
1
vote
1
reply
57
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 3 hours ago by
Ram
43k • written 4 hours ago by
Pumla
• 0
0
votes
0
replies
50
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated 13 minutes ago by
Ram
43k • written 10 hours ago by
SAsciences
• 0
0
votes
0
replies
50
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
5 hours ago by
liuyibin2005
• 0
0
votes
1
reply
45
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 2 hours ago by
ATpoint
81k • written 3 hours ago by
gdfsnkfns
• 0
0
votes
0
replies
41
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
5 hours ago by
blur
▴ 280
0
votes
0
replies
38
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
4 hours ago by
Broccoli
• 0
0
votes
0
replies
38
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 10 minutes ago by
Ram
43k • written 6 hours ago by
M'zelle
• 0
0
votes
0
replies
31
views
Training
chip-seq
ScATAC-seq
2 hours ago by
Manhezz
• 0
0
votes
0
replies
21
views
How to change alternate conformation occupancy ?
Module
Bio.PDB.Atom
Bio.PDB
updated 1 hour ago by
GenoMax
140k • written 1 hour ago by
udakshi
• 0
0
votes
0
replies
20
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
1 hour ago by
Picasa
▴ 640
0
votes
1
reply
15
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 10 minutes ago by
Ram
43k • written 34 minutes ago by
chiditatawmbi
• 0
33 results • Page
1 of 1
Recent Votes
Comment: Only one read per run - Trying to use CellRangerv7
Comment: Interproscan taking so much time
Answer: Interproscan taking so much time
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
A: Crispr-cas9 screen analysis mageck
A: Crispr-cas9 screen analysis mageck
Crispr-cas9 screen analysis mageck
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Commentator
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Devon Ryan
104k
Popular Question
to
amitpande74
▴ 20
Scholar
to
Pierre Lindenbaum
160k
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beacamara
• 0
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blur
▴ 280
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ATpoint
81k
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Haci
▴ 550
Recent Replies
Answer: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did ran the "JoinLayers()" even then it is not working, here is the output before and after ``` DefaultAssay(combined1) <- 'RNA' combin…
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
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Share code and an example please.
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
Comment: Interproscan taking so much time
by
Mohamed Abderrahmane
▴ 10
Thank you for your reply. I have just executed the computation with parallelization as you mentioned, and I will observe the differences. H…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
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