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1,113 results • Page
2 of 23
Sort: replies
Rank
Views
Votes
Replies
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 4 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 16 days ago by
Aspire
▴ 320 • written 18 months ago by
Manav
• 0
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 21 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 13 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
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 14 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 1 day ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
3
votes
10
replies
647
views
Piping samtools to R
R
NGS
bash
samtools
14 days ago by
noodle
▴ 580
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 14 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 25 days ago by
Ram
43k • written 6.4 years ago by
J.F.Jiang
▴ 920
1
vote
10
replies
962
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
6 days ago by
DKA
▴ 40
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 12 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 14 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
8
votes
10
replies
732
views
bash script
whole-genome-sequencing
updated 15 days ago by
Ram
43k • written 23 days ago by
bestone
▴ 30
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 21 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 15 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
0
votes
10
replies
471
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 8 days ago by
Patadu94
• 0
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 25 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
3
votes
9
replies
483
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 6 days ago by
Istvan Albert
100k • written 8 days ago by
Κοσμάς
• 0
1
vote
9
replies
550
views
Can index hopping lead to more reads in samples?
index-hopping
NovoSeq
illumina
NGS
Seqeucning
25 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 13 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 18 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
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 13 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
3
votes
9
replies
856
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 12 days ago by
Elisabeth Gasteiger
★ 2.4k • written 13 days ago by
Jacky
• 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 2 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
9
replies
858
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 7 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
9
replies
563
views
frequency of each variant per sample
freebayes
variant-frequency
updated 26 days ago by
Pierre Lindenbaum
161k • written 27 days ago by
emilydolivo97
▴ 10
4
votes
9
replies
588
views
variant calling
variant-calling
updated 27 days ago by
Ram
43k • written 28 days ago by
dalibenam64
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
1 day ago by
anna
▴ 20
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
0
votes
9
replies
607
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 19 days ago by
LauferVA
4.2k • written 20 days ago by
Aki
▴ 20
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 14 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 14 days ago by
Ram
43k • written 5.8 years ago by
fp89
▴ 30
7
votes
8
replies
676
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 18 days ago by
spen
▴ 40 • written 22 days ago by
MBarcelo
▴ 40
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 12 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
0
votes
8
replies
385
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 16 hours ago by
LauferVA
4.2k • written 2 days ago by
jinyu
▴ 10
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 12 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
6
votes
8
replies
584
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 14 days ago by
dariober
14k • written 16 days ago by
manaswiniparija3
▴ 40
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 21 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 21 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
8
votes
8
replies
615
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
Aaliya
▴ 10
1
vote
8
replies
830
views
Adding CB tag to bam file
samtools
bam
updated 6 days ago by
Pierre Lindenbaum
161k • written 12 days ago by
Maria
• 0
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 11 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
1
vote
8
replies
700
views
6 follow
Finding insert sequences using long reads
insert-sequences
Nanopore
long-read-assembly
updated 21 days ago by
Anand Rao
▴ 630 • written 8 weeks ago by
bvm
▴ 20
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 13 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
8
replies
563
views
FreeBayes encountered a sudden error
freebayes
updated 26 days ago by
Michael
54k • written 26 days ago by
emilydolivo97
▴ 10
4
votes
8
replies
621
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 4 days ago by
Alex Reynolds
35k • written 5 days ago by
J
▴ 10
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 23 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
7
votes
8
replies
683
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
26 days ago by
Riq
▴ 50
1
vote
8
replies
420
views
Downsampling fastq file
downsample
fastq
19 hours ago by
marco.barr
▴ 80
17
votes
8
replies
13k
views
9 follow
MAF vs VAF
sequencing
updated 28 days ago by
AshleeThomson
▴ 80 • written 6.1 years ago by
lauren.wahyudi
▴ 50
1,113 results • Page
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Recent Votes
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
Answer: Discrepancy between Log2(x) and Log2(x+1) regarding Log2FC
Answer: Verify if all the components of a pathway are present in a genomes
Answer: p-value in CIBERSORT
Answer: Can I have multiple active GDC download tokens?
Answer: Can I have multiple active GDC download tokens?
Comment: Can I have multiple active GDC download tokens?
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Comment: Post-imputation plot
by
kl
▴ 10
All of them are G/C and A/T variants Some seem mismatches based on AF and some seem to need flipping. I guess I am confused, as in the Mich…
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
Nafi
• 0
Thank you for the reply I have 16 gb of RAM then I can give a try then.
Comment: Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
by
i.sudbery
19k
Can you give more details of the data you are planning to use. What is the different studies, what are the comparisons you want to make.
Comment: p-value in CIBERSORT
by
michelafrancesconi9
▴ 20
Thank you so much!!
Comment: POSSUM not working due to incompatible pssm file
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: after selecting specific GO terms to plot, cneplot is not showing any color for
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Telescope issue
by
GenoMax
141k
Looks like there is a tab missing between the sequence and the quality string.
Comment: Post-imputation plot
by
LChart
3.9k
I would pull out the variants with panel_freq ~ 1 - upload_freq and min(panel_freq, upload_freq) < 0.4. I would check if these are G/C or A…
Comment: Telescope issue
by
eleven11
• 0
Hello the output is A01940:33:GW2208142379th:3:1317:24126:3505 355 chr14 16651125 0 150M = 17034150 122900 GCTAACAGAGTTGAACCTTTCTATTG…
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
Looking at the [code here][1] `bundle_uuid` seems to be related to the submissions to HCA. Samples that ran on multiple lanes seem to have …
Comment: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
jeffrey.maurer.informatics
• 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT
by
Aspire
▴ 320
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
Comment: Telescope issue
by
GenoMax
141k
> CIGAR and query sequence are of different length [W::sam_read1] Parse error at line 9954941 Problem appears to be at that line. Can you …
Comment: KEGG Pathways
by
Ram
43k
Give us as much detail as you can. What error does it give you?
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