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16 results • Page
1 of 1
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6
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5
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2.3k
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Tophat multiple or unique mapping criteria
RNA-Seq
updated 8 hours ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
3
votes
6
replies
426
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 3 hours ago by
Pine
▴ 20 • written 7 days ago by
snajafy
• 0
1
vote
5
replies
412
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 3 hours ago by
arctic
▴ 40 • written 9 days ago by
M.
▴ 30
0
votes
11
replies
390
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
2 hours ago by
Tuck898
• 0
0
votes
6
replies
297
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
plink
bioinformatics
genomics
updated 4 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
ajbarrett98
• 0
6
votes
7
replies
248
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
2 hours ago by
sansan_96
▴ 90
0
votes
2
replies
218
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
10 hours ago by
beginner123
• 0
2
votes
8
replies
198
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 7 hours ago by
Pierre Lindenbaum
161k • written 10 hours ago by
Matteo Ungaro
▴ 100
0
votes
1
reply
171
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 23 hours ago by
Mathew
▴ 100 • written 1 day ago by
Christopher
• 0
0
votes
1
reply
166
views
input file in rmats
rmats
updated 15 hours ago by
Mathew
▴ 100 • written 2 days ago by
Lambodarswain316
• 0
0
votes
1
reply
146
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 6 hours ago by
pjb39
▴ 200 • written 2 days ago by
beantkapoor16
• 0
0
votes
2
replies
111
views
Output file of satools flagstat empty
samtools-flagstat
updated 6 hours ago by
Mathew
▴ 100 • written 8 hours ago by
ramendra.sarma
• 0
0
votes
1
reply
84
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
batch
ComBat-seq
limma
RNA-seq
removeBatchEffect
updated 47 minutes ago by
ATpoint
82k • written 5 hours ago by
t.fortunato.asquini
• 0
0
votes
0
replies
63
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
14 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
43
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
7 hours ago by
BioinfGuru
★ 1.7k
0
votes
0
replies
31
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
4 hours ago by
rackbersingh
• 0
16 results • Page
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Recent Votes
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
Answer: install package
Answer: How I do lift over a Plink bim file from Hg18 to Hg19.
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
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pjb39
▴ 200
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Recent Replies
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
by
ATpoint
82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Pine
▴ 20
This seems to indicate that the R verison you are using (or packages it depends on) are not compatible with the R version you are using any…
Answer: Tissue-specific DEG analysis with DEseq2
by
arctic
▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
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
▴ 100
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…
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