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116,727 results • Page
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53
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Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 3 hours ago by
Qroid
▴ 40 • written 4 hours ago by
Qi
• 0
0
votes
2
replies
73
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 4 hours ago by
harold.smith.tarheel
★ 4.9k • written 6 hours ago by
SJP
• 0
0
votes
0
replies
26
views
Empty table plot using plotGseaTable()
FGSEA
4 hours ago by
Chris
▴ 260
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
71
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 5 hours ago by
anovak
▴ 120 • written 9 hours ago by
Hang
• 0
1
vote
3
replies
120
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 5 hours ago by
jared.andrews07
★ 16k • written 9 hours ago by
yvonneh
▴ 10
1
vote
2
replies
79
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
5 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 6 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
86
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
6 hours ago by
dtnondorf
• 0
0
votes
0
replies
51
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
7 hours ago by
sovrappensiero
▴ 90
0
votes
1
reply
98
views
RNA-seq data for deep learning classification
rna-seq
updated 8 hours ago by
dsull
★ 5.9k • written 10 hours ago by
Yuju
• 0
2
votes
6
replies
180
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
1 hour ago by
Qroid
▴ 40
0
votes
1
reply
442
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 9 hours ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
75
views
Provean help
variant
Provean
updated 6 hours ago by
Mensur Dlakic
★ 27k • written 10 hours ago by
Arun Sai Kumar
• 0
1
vote
1
reply
101
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 10 hours ago by
bk11
★ 2.4k • written 19 hours ago by
Jeol
▴ 20
1
vote
1
reply
107
views
Super ehancers
enhancers
updated 10 hours ago by
jared.andrews07
★ 16k • written 15 hours ago by
Oburah
• 0
0
votes
4
replies
141
views
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 10 hours ago by
jared.andrews07
★ 16k • written 11 hours ago by
JH
• 0
0
votes
2
replies
114
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
8 hours ago by
Chen
• 0
5
votes
5
replies
192
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 11 hours ago by
atharvakarkare14
▴ 30 • written 14 hours ago by
Begonia_pavonina
▴ 150
0
votes
6
replies
340
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
updated 11 hours ago by
GenoMax
142k • written 22 days ago by
eesiribloom
▴ 80
1
vote
1
reply
105
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 10 hours ago by
Ram
43k • written 13 hours ago by
alifafiq1
• 0
0
votes
0
replies
57
views
Use of annotation of integrated Seurat object in single sample
Seurat
15 hours ago by
Bine
▴ 60
0
votes
0
replies
60
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 10 hours ago by
Ram
43k • written 15 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
179
views
Subsetting and merging back Seurat Object brings different results
Seurat
12 hours ago by
Bine
▴ 60
0
votes
0
replies
81
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 10 hours ago by
Ram
43k • written 16 hours ago by
4r-rtg
• 0
1
vote
1
reply
102
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 10 hours ago by
Ram
43k • written 16 hours ago by
marco.barr
▴ 90
0
votes
0
replies
54
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
17 hours ago by
Rhiannon
• 0
0
votes
1
reply
98
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 7 hours ago by
Ram
43k • written 19 hours ago by
nithya
• 0
0
votes
0
replies
62
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
19 hours ago by
Vijith
▴ 30
9
votes
10
replies
411
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 9 hours ago by
Zamin Iqbal
▴ 20 • written 1 day ago by
nicole.kavanagh
• 0
0
votes
1
reply
238
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 21 hours ago by
Scooter
▴ 280 • written 7 days ago by
avocado123
• 0
0
votes
0
replies
63
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
22 hours ago by
James
▴ 10
0
votes
1
reply
554
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 23 hours ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
2
replies
150
views
Odd alignment question/finding
Alignment
updated 17 hours ago by
ATpoint
82k • written 23 hours ago by
poordumbsillyidiot
• 0
0
votes
1
reply
172
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 1 day ago by
GenoMax
142k • written 1 day ago by
mgranada3
▴ 30
0
votes
0
replies
69
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
1 day ago by
meck
• 0
0
votes
0
replies
96
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
7
replies
442
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 50 minutes ago by
LChart
3.9k • written 3 days ago by
kl
▴ 10
0
votes
1
reply
186
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
J
• 0
1
vote
3
replies
264
views
DESeq2 processing problems
deseq2
R
updated 1 day ago by
ATpoint
82k • written 1 day ago by
jagdish7921
• 0
0
votes
1
reply
755
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 10 hours ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
118
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
86
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 0
1
vote
2
replies
222
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
20 hours ago by
rianna.collins
• 0
0
votes
1
reply
157
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
123
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
454
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
2
votes
2
replies
247
views
p-value in CIBERSORT
CIBERSORT
p-value
1 day ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
329
views
Telescope issue
Telescope
RNA-seq
updated 1 day ago by
GenoMax
142k • written 2 days ago by
eleven11
• 0
5
votes
6
replies
489
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 2 days ago by
me
▴ 760 • written 3 days ago by
Mariana
▴ 40
116,727 results • Page
1 of 2335
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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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Comment: Post-imputation plot
by
LChart
3.9k
Imputation takes what? A day or two of compute time? Just re-do it.
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thanks. Really appreciate your help with this. This site is such a great resource. The methods aren't totally clear on how they're gettin…
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 --…
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