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119 results • Page
3 of 3
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Votes
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0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 22 hours ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 9 hours ago by
Ram
43k • written 6.0 years ago by
Jun
• 0
0
votes
1
reply
141
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 9 hours ago by
GenoMax
141k • written 9 hours ago by
Kai Xin
• 0
0
votes
2
replies
162
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
47 minutes ago by
feather-W
• 0
0
votes
2
replies
149
views
How can I solve this error?
metal
46 minutes ago by
22211020193
• 0
0
votes
0
replies
67
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 9 hours ago by
Ram
43k • written 9 hours ago by
otieno43
▴ 20
0
votes
0
replies
2.6k
views
Removing batch effects from methylation beta values for molecular subtyping/cluster analysis
clustering
beta-values
batch-effect
methylation
updated 23 hours ago by
Ram
43k • written 6.7 years ago by
alecmchiu
• 0
0
votes
1
reply
106
views
Freyja plot error
Freyja
updated 12 hours ago by
Ram
43k • written 18 hours ago by
Adyasha
• 0
0
votes
3
replies
1.1k
views
Discrepancy between E() Values in Blastp Search - HELP
BLAST
E-value
Blastp
Protein
updated 12 hours ago by
Ram
43k • written 5.3 years ago by
minasmayth
• 0
0
votes
2
replies
167
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
updated 12 hours ago by
colindaven
6.3k • written 17 hours ago by
valentinatsar
• 0
0
votes
1
reply
2.7k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 7 hours ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
2
replies
326
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
12 hours ago by
arriyaz.nstu
▴ 30
0
votes
1
reply
255
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 11 hours ago by
Klaus S
▴ 150 • written 5 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
74
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 10 hours ago by
GenoMax
141k • written 11 hours ago by
srimmer
• 0
0
votes
1
reply
116
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 6 hours ago by
GenoMax
141k • written 6 hours ago by
ycts
• 0
0
votes
1
reply
176
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 10 hours ago by
bk11
★ 2.3k • written 1 day ago by
航太郎
• 0
0
votes
8
replies
327
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 10 hours ago by
Pierre Lindenbaum
161k • written 13 hours ago by
me
• 0
0
votes
3
replies
179
views
biomaRt error for different R version
biomaRt
R
updated 14 hours ago by
Mike Smith
★ 2.0k • written 18 hours ago by
manaswwm
▴ 490
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA
RNA-Seq
batch-effect
updated 23 hours ago by
Ram
43k • written 8.5 years ago by
annadv
• 0
119 results • Page
3 of 3
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Error with Formatdb of legacy blast?
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Recent Replies
Comment: ISCN annotation for SV/CN VCF files
by
adedare
• 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error?
by
22211020193
• 0
I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results?
by
feather-W
• 0
Hi LChart, Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates
by
joe
▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis
by
geneontologyhelp
▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data?
by
etiennedanis
▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates
by
joe
▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
by
GenoMax
141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
swbarnes2
14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
by
quentinperriere
• 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Answer: Inconsistency in SNP detection pipelines for multi-sample analysis
by
LChart
3.9k
> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option I'm not sure what you m…
Comment: Supergnova stuck in tutorial
by
GenoMax
141k
Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★ 1.7k
Thanks @lchart, I accept that, I'll wait to see if there's any more who want to input and then accept the answer
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