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85 results • Page
1 of 2
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0
votes
1
reply
35
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 1 hour ago by
Qroid
▴ 40 • written 2 hours ago by
Qi
• 0
0
votes
0
replies
17
views
Empty table plot using plotGseaTable()
FGSEA
2 hours ago by
Chris
▴ 260
1
vote
2
replies
73
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
3 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 4 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
80
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
4 hours ago by
dtnondorf
• 0
0
votes
0
replies
44
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
5 hours ago by
sovrappensiero
▴ 90
2
votes
5
replies
148
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
updated just now by
GenoMax
142k • written 7 hours ago by
Qroid
▴ 40
0
votes
1
reply
70
views
Provean help
variant
Provean
updated 4 hours ago by
Mensur Dlakic
★ 27k • written 7 hours ago by
Arun Sai Kumar
• 0
0
votes
0
replies
53
views
Use of annotation of integrated Seurat object in single sample
Seurat
13 hours ago by
Bine
▴ 60
0
votes
1
reply
176
views
Subsetting and merging back Seurat Object brings different results
Seurat
10 hours ago by
Bine
▴ 60
1
vote
1
reply
100
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 7 hours ago by
Ram
43k • written 14 hours ago by
marco.barr
▴ 90
0
votes
0
replies
51
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
15 hours ago by
Rhiannon
• 0
0
votes
1
reply
96
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 5 hours ago by
Ram
43k • written 17 hours ago by
nithya
• 0
0
votes
0
replies
60
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
17 hours ago by
Vijith
▴ 30
0
votes
0
replies
61
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
19 hours ago by
James
▴ 10
0
votes
1
reply
552
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 21 hours ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
2
replies
148
views
Odd alignment question/finding
Alignment
updated 15 hours ago by
ATpoint
82k • written 21 hours ago by
poordumbsillyidiot
• 0
0
votes
1
reply
170
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
mgranada3
▴ 30
0
votes
0
replies
67
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
1 day ago by
meck
• 0
0
votes
0
replies
94
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 1 day ago by
Ram
43k • written 1 day ago by
Oscar
▴ 10
0
votes
1
reply
116
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
84
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 0
1
vote
2
replies
220
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
18 hours ago by
rianna.collins
• 0
0
votes
1
reply
155
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 1 day ago by
i.sudbery
19k • written 2 days ago by
Edmond
• 0
0
votes
0
replies
121
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
2 days ago by
O.rka
▴ 710
0
votes
1
reply
442
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 1 day ago by
Ram
43k • written 2 days ago by
Dr Huma Naz
• 0
0
votes
5
replies
326
views
Telescope issue
Telescope
RNA-seq
updated 1 day ago by
GenoMax
142k • written 2 days ago by
eleven11
• 0
1
vote
1
reply
214
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 2 days ago by
Ram
43k • written 2 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
271
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
1 day ago by
Nafi
• 0
1
vote
3
replies
257
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jeffrey.maurer.informatics
• 0
0
votes
1
reply
168
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
121
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
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
1
reply
157
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
3
replies
261
views
KEGG Pathways
r
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Sudip
• 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
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 days ago by
8armed
• 0
1
vote
2
replies
212
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
0
replies
106
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
0
votes
0
replies
110
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
0
replies
123
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
1
reply
176
views
Differential Accessibility
DiffBind
updated 3 days ago by
Ram
43k • written 3 days ago by
Shloka
• 0
0
votes
3
replies
266
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
kim
• 0
3
votes
7
replies
312
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 days ago by
salias
• 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
Synteny analysis
bacterial
synteny
genome
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Namil
• 0
0
votes
4
replies
236
views
Genbank File Format
gbkformat
2 days ago by
alenew.am
• 0
0
votes
0
replies
215
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
3 days ago by
SSSJec
• 0
0
votes
3
replies
207
views
Software to separate reads from different individuals
software
development
nanopore
updated 3 days ago by
GenoMax
142k • written 3 days ago by
njornet
▴ 20
0
votes
0
replies
91
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
85 results • Page
1 of 2
Recent Votes
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
How to convert plink data from 38th assembly to 37
How to convert plink data from 38th assembly to 37
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
Comment: Converting CRAM to FastQ
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Recent Replies
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
Comment: Does comparing two different groups to a common third group introduce bias in th
by
Qroid
▴ 40
Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
Answer: Bedtools merge minimum overlap?
by
harold.smith.tarheel
★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
by
bk11
★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa
by
anovak
▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
Answer: DiffBind: no peaks in DBA
by
jared.andrews07
★ 16k
Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation? In addition, a ChIP-seq experiment…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ
by
GenoMax
142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
No that was only from Breast cancer. You could try selecting all data and see if you are able to see all treatments in the set. No idea a…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as you …
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