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88 results • Page
2 of 2
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0
votes
2
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147
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
3 days ago by
Lluís R.
★ 1.2k
1
vote
2
replies
140
views
Odd alignment question/finding
Alignment
updated 11 hours ago by
ATpoint
82k • written 17 hours ago by
poordumbsillyidiot
• 0
0
votes
0
replies
138
views
Filter low express genes in microarray data
microarray
4 days ago by
Chris
▴ 260
0
votes
0
replies
134
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
4 days ago by
tnminh89
▴ 10
0
votes
1
reply
127
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Winter
• 0
0
votes
0
replies
123
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
2 days ago by
Bine
▴ 60
0
votes
0
replies
123
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 days ago by
8armed
• 0
0
votes
0
replies
120
views
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
0
replies
120
views
Using limma in methylation EM-seq?
EM-seq
methylation
3 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
120
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
0
replies
117
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 3 days ago by
dariober
14k • written 4 days ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 2 days ago by
Alexandros
• 0
0
votes
0
replies
113
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
1 day ago by
O.rka
▴ 710
0
votes
0
replies
109
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
2 days ago by
fanglujing
▴ 60
0
votes
1
reply
106
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 1 day ago by
Ram
43k • written 1 day ago by
ernestine.kubi
• 0
0
votes
0
replies
105
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
0
votes
0
replies
99
views
LEfSe
LEfSe
3 days ago by
benkosta
• 0
0
votes
0
replies
96
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
3 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
92
views
vg call vs vg surject
vg
variation
graphs
updated 3 days ago by
GenoMax
142k • written 3 days ago by
aliraza3119
• 0
0
votes
0
replies
90
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
1
vote
1
reply
89
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 3 hours ago by
Ram
43k • written 10 hours ago by
marco.barr
▴ 90
0
votes
1
reply
88
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 50 minutes ago by
Ram
43k • written 12 hours ago by
nithya
• 0
0
votes
0
replies
86
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 21 hours ago by
Ram
43k • written 22 hours ago by
Oscar
▴ 10
0
votes
0
replies
86
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
3 days ago by
Sara
▴ 30
0
votes
0
replies
86
views
Differential accessibility using DiffBinf
diffbind
3 days ago by
Shloka
• 0
0
votes
0
replies
75
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 0
0
votes
0
replies
61
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
22 hours ago by
meck
• 0
0
votes
0
replies
53
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
13 hours ago by
Vijith
▴ 30
0
votes
0
replies
53
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
15 hours ago by
James
▴ 10
1
vote
2
replies
54
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
16 minutes ago by
Qroid
▴ 40
1
vote
2
replies
45
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
1 hour ago by
yvonneh
▴ 10
0
votes
0
replies
43
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
10 hours ago by
Rhiannon
• 0
0
votes
0
replies
43
views
Use of annotation of integrated Seurat object in single sample
Seurat
8 hours ago by
Bine
▴ 60
0
votes
1
reply
31
views
Provean help
variant
Provean
updated 10 minutes ago by
Mensur Dlakic
★ 27k • written 3 hours ago by
Arun Sai Kumar
• 0
0
votes
2
replies
24
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
20 minutes ago by
dtnondorf
• 0
0
votes
0
replies
22
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
2 hours ago by
Hang
• 0
0
votes
0
replies
18
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
1 hour ago by
sovrappensiero
▴ 90
88 results • Page
2 of 2
Recent Votes
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Comment: How to access TCGA samples that were treated with a specific drug?
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Comment: Provean help
by
Mensur Dlakic
★ 27k
> Else, I will happy to send over the data and kindly perform the analysis for me. This website is meant to provide advice, not service. I…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thank you! Naive question, but does that list include all treatments in TCGA? I.e. is there anything missing from there, or that's it? Als…
Comment: Base Quality Score Recalibration with different reference genome
by
dtnondorf
• 0
Interesting! Thank you for such a quick response!
Comment: GATK genomicsDBimport intervals for WGS
by
Sd
• 0
I also have similar question. I sliced the genomic bed file with 50kb windows and 1kb padding into ~700 bed files; each bed file contains 9…
Comment: Base Quality Score Recalibration with different reference genome
by
GenoMax
142k
See answer here: https://www.biostars.org/p/9494503/#9494619 Heng Li said: https://twitter.com/lh3lh3/status/1410375781340135424 <!-- th…
Comment: DiffBind: no peaks in DBA
by
yvonneh
▴ 10
Ok fixed!
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
Can you try lowering the `k` to `k=9`? You don't have any duplicate sequences in your library file? That may be one reason why bbduk is r…
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
This topic is almost 5 years old, but I am facing the same (or at least a very similar) issue. I have ngs files from a CRISPR screen that …
Answer: RNA-seq data for deep learning classification
by
dsull
★ 5.9k
Honestly speaking, if it's deep learning, it probably doesn't matter that much if you use something like TPMs (probably not raw counts, unl…
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
Thanks for the detailed answer and I really appreciate it! I still have one question about why the number of reads can be influenced by the…
Comment: Split Fastq Files Into Chunks Of 1M Reads
by
thomas.heigl.ibk
• 0
i tried it. it splits, however, when i compare the first 8 lines of the second split file with the according lines from the original file, …
Comment: DiffBind: no peaks in DBA
by
Ram
43k
> I've also included the txt version of my .csv file No, you added a screenshot of plain text content, which is counterproductive. You can…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
At the GDC portal you have to turn the "therapeutic agents" toggle under "Clinical Data Analysis" on. ![drug][1] For Breast cancer you c…
Answer: Loss of 'var' using concatenation of AnnData objects
by
Hugo
• 0
Similar question has been asked and answered on [scverse discourse](https://discourse.scverse.org/t/loosing-anndata-var-layer-when-using-sc…
Comment: Bacterial plasmid analysis
by
Zamin Iqbal
▴ 20
Hi Nicole. 1. The clustering will be quite different between pling and the rep types (because plasmids with one rep type can still be ve…
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