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14 results • Page
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How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
batch
ComBat-seq
limma
RNA-seq
removeBatchEffect
10 minutes ago by
t.fortunato.asquini
• 0
0
votes
1
reply
121
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 48 minutes ago by
pjb39
▴ 200 • written 1 day ago by
beantkapoor16
• 0
0
votes
2
replies
66
views
Output file of satools flagstat empty
samtools-flagstat
updated 1 hour ago by
Mathew
▴ 90 • written 3 hours ago by
ramendra.sarma
• 0
0
votes
0
replies
24
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
2 hours ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
152
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 1 hour ago by
Pierre Lindenbaum
161k • written 5 hours ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
48
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
9 hours ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
150
views
input file in rmats
rmats
updated 10 hours ago by
Mathew
▴ 90 • written 2 days ago by
Lambodarswain316
• 0
0
votes
1
reply
160
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 18 hours ago by
Mathew
▴ 90 • written 1 day ago by
Christopher
• 0
6
votes
6
replies
211
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
updated 12 hours ago by
Mathew
▴ 90 • written 18 hours ago by
sansan_96
▴ 90
2
votes
2
replies
147
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
updated 19 hours ago by
Mathew
▴ 90 • written 21 hours ago by
Azra
▴ 10
0
votes
2
replies
198
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 hours ago by
beginner123
• 0
0
votes
4
replies
253
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
20 hours ago by
ajbarrett98
• 0
1
vote
4
replies
350
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 hour ago by
BioinfGuru
★ 1.7k • written 9 days ago by
M.
▴ 30
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 3 hours ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
14 results • Page
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Recent Votes
Answer: joint callset and vcf sorting, unknown TAG issue
Answer: joint callset and vcf sorting, unknown TAG issue
A: what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
A: what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean
Gff To Vcf
Comment: Longest transcript variant per gene
Comment: Longest transcript variant per gene
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Recent Awards •
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pjb39
▴ 200
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Jen
▴ 70
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Pierre Lindenbaum
161k
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Recent Replies
Answer: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty
by
Mathew
▴ 90
Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Comment: Tissue-specific DEG analysis with DEseq2
by
BioinfGuru
★ 1.7k
I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> set the Number= to 0 instead of 1; I'm not sure it's a problem. > probably I should also change the Type to Flag ah yes, my bad ! (f…
Comment: Output file of satools flagstat empty
by
GenoMax
142k
If you posted the entire command line then you did not include `-O $MAPPING/${i}.mapping_stats.txt` in that.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum I see. I looked up and, although present, the TAG goes like this in both files: `##INFO=<ID=1000gALT,Number=0,Type=Flag,…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum much appreciated, thanks for the explanation and possible approaches to solve this. I'm not in the position to run `U…
Comment: Tophat multiple or unique mapping criteria
by
Ruqaiya
• 0
> The --b2-mp defines the mismatch penalty: the first number is used when the quality of the base is good, the second when it's bad. If you…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> Still, I can't understand the Invalid tag name: "1000gALT" the following line is missing in the VCF header: ##INFO=<ID=1000gALT,Num…
Answer: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
INFO at 121387974 is .;CpG this is an invalid INFO column. There is an invalid attribute named '.' followed by the attribute CpG, …
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum as I don't know the meaning of `.;` and I've seen there are many in both files, I simply removed them with `grep -v`. …
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴ 100
My bad I switched positions between the two files when looking the first time. They do indeed look abnormal but how can I fix it? Below the…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
beginner123
• 0
Hi, no I'm using the python implementation as linked above.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
Show us the content of the INFO column at the problematic positions.
Comment: Tissue-specific DEG analysis with DEseq2
by
ATpoint
82k
Sounds like full confounding. Be careful. Personally I would not do this comparison. There is no way to distinguish tissue effect from dono…
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