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1,066 results • Page
2 of 22
Sort: replies
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Votes
Replies
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 27 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
1
vote
10
replies
974
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
8 days ago by
DKA
▴ 40
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 3 days ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 15 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
8
votes
10
replies
751
views
bash script
whole-genome-sequencing
updated 17 days ago by
Ram
43k • written 24 days ago by
bestone
▴ 30
0
votes
10
replies
485
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 10 days ago by
Patadu94
• 0
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 16 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 14 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 23 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 15 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 17 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 15 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
9
votes
10
replies
409
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 8 hours ago by
Zamin Iqbal
▴ 20 • written 1 day ago by
nicole.kavanagh
• 0
3
votes
10
replies
650
views
Piping samtools to R
R
NGS
bash
samtools
15 days ago by
noodle
▴ 580
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 27 days ago by
Ram
43k • written 6.5 years ago by
J.F.Jiang
▴ 920
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 23 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 18 days ago by
Aspire
▴ 330 • written 18 months ago by
Manav
• 0
4
votes
9
replies
595
views
variant calling
variant-calling
updated 29 days ago by
Ram
43k • written 4 weeks ago by
dalibenam64
• 0
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 15 days ago by
Ram
43k • written 5.8 years ago by
fp89
▴ 30
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 19 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
3 days ago by
anna
▴ 20
11
votes
9
replies
7.0k
views
How to choose method to integrate different patient sample together in Seurat
Seurat
scRNA
batch-effect
harmony
updated 15 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 3 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
3
votes
9
replies
496
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 8 days ago by
Istvan Albert
100k • written 10 days ago by
Κοσμάς
• 0
3
votes
9
replies
875
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 14 days ago by
Elisabeth Gasteiger
★ 2.4k • written 14 days ago by
Jacky
• 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 15 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
9
replies
613
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 21 days ago by
LauferVA
4.2k • written 22 days ago by
Aki
▴ 20
2
votes
9
replies
865
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 8 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 14 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
1
vote
9
replies
554
views
Can index hopping lead to more reads in samples?
index-hopping
NovoSeq
illumina
NGS
Seqeucning
27 days ago by
Assa Yeroslaviz
★ 1.8k
2
votes
9
replies
567
views
frequency of each variant per sample
freebayes
variant-frequency
updated 28 days ago by
Pierre Lindenbaum
161k • written 29 days ago by
emilydolivo97
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 5 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
1
vote
8
replies
854
views
Adding CB tag to bam file
samtools
bam
updated 7 days ago by
Pierre Lindenbaum
161k • written 14 days ago by
Maria
• 0
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 22 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 14 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
7
votes
8
replies
681
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 20 days ago by
spen
▴ 40 • written 23 days ago by
MBarcelo
▴ 40
1
vote
8
replies
440
views
Downsampling fastq file
downsample
fastq
2 days ago by
marco.barr
▴ 90
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 24 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
17
votes
8
replies
13k
views
9 follow
MAF vs VAF
sequencing
updated 29 days ago by
AshleeThomson
▴ 80 • written 6.1 years ago by
lauren.wahyudi
▴ 50
8
votes
8
replies
627
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 7 days ago by
swbarnes2
14k • written 8 days ago by
Aaliya
▴ 10
4
votes
8
replies
642
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 5 days ago by
Alex Reynolds
35k • written 6 days ago by
J
▴ 10
0
votes
8
replies
365
views
Error in cnetplot enrichplot package
R
updated 10 days ago by
Ram
43k • written 10 days ago by
Farhad
• 0
1
vote
8
replies
703
views
6 follow
Finding insert sequences using long reads
insert-sequences
Nanopore
long-read-assembly
updated 23 days ago by
Anand Rao
▴ 630 • written 8 weeks ago by
bvm
▴ 20
0
votes
8
replies
419
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 2 days ago by
LauferVA
4.2k • written 4 days ago by
jinyu
▴ 10
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 14 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 23 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 15 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
8
replies
573
views
FreeBayes encountered a sudden error
freebayes
updated 27 days ago by
Michael
54k • written 28 days ago by
emilydolivo97
▴ 10
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 12 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
1,066 results • Page
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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: 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
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★ 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
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★ 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
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> 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
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▴ 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 …
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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…
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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…
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by
Maverick
▴ 10
Thank you so much! Will look it up right away.
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> 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…
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by
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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…
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