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24 results • Page
1 of 1
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Views
Votes
Replies
0
votes
0
replies
13
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
56 minutes ago by
rianna.collins
• 0
0
votes
0
replies
20
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
2 hours ago by
Edmond
• 0
0
votes
0
replies
26
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
3 hours ago by
O.rka
▴ 710
0
votes
2
replies
103
views
Telescope issue
Telescope
RNA-seq
5 hours ago by
eleven11
• 0
0
votes
0
replies
54
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 5 hours ago by
Ram
43k • written 8 hours ago by
J
• 0
0
votes
0
replies
57
views
Defined objects of type "S4" error in single cell analysis
Seurat
single-cell
DoubletFinder
single-nuclei
SeuratObject
10 hours ago by
sarphilsar
• 0
0
votes
1
reply
106
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 5 hours ago by
Ram
43k • written 10 hours ago by
Jonathan Yoou
▴ 60
0
votes
1
reply
116
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
updated 5 hours ago by
Ram
43k • written 10 hours ago by
Nafi
• 0
0
votes
3
replies
135
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 5 hours ago by
GenoMax
141k • written 10 hours ago by
jeffrey.maurer.informatics
• 0
0
votes
0
replies
68
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 11 hours ago by
Ram
43k • written 13 hours ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
63
views
barcode of TCR-sequencing
barcode
13 hours ago by
yueli7
▴ 250
0
votes
0
replies
65
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 12 hours ago by
Ram
43k • written 15 hours ago by
Alexandros
• 0
0
votes
1
reply
95
views
unable to get feature count results
featureCounts
updated 11 hours ago by
Ram
43k • written 15 hours ago by
Ravita
• 0
0
votes
0
replies
65
views
Subsetting and merging back Seurat Object brings different results
Seurat
15 hours ago by
Bine
▴ 60
0
votes
3
replies
178
views
KEGG Pathways
r
RNA-seq
updated 8 hours ago by
Ram
43k • written 16 hours ago by
Sudip
• 0
0
votes
0
replies
68
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
16 hours ago by
Bine
▴ 60
0
votes
0
replies
68
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
17 hours ago by
8armed
• 0
1
vote
2
replies
156
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 10 hours ago by
Ram
43k • written 19 hours ago by
Ravita
• 0
0
votes
0
replies
61
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
19 hours ago by
Adyasha
• 0
0
votes
0
replies
65
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
22 hours ago by
fanglujing
▴ 60
0
votes
3
replies
217
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 14 hours ago by
GenoMax
141k • written 1 day ago by
kim
• 0
0
votes
4
replies
199
views
Genbank File Format
gbkformat
18 hours ago by
alenew.am
• 0
1
vote
8
replies
409
views
Downsampling fastq file
downsample
fastq
9 hours ago by
marco.barr
▴ 80
0
votes
10
replies
465
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 16 hours ago by
i.sudbery
19k • written 8 days ago by
Patadu94
• 0
24 results • Page
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Recent Votes
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?
Comment: Programmatically retrieving positions of protein active site residues
Comment: Programmatically retrieving positions of protein active site residues
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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?
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
SRA Run Selector shows a better view of the metadata: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA761679&o=acc_s%3Aa
Comment: Adjust pvalue in R with different approach give me all different outcome
by
Aspire
▴ 320
- `p.adjust()` is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, …
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I understood where the problem lies. I discussed with my wet lab colleagues (this is part of a bioinformatician's job...) and by showing th…
Comment: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This question fits in nicely with the [SIB Swiss Institute of Bioinformatics course on Enzyme information in UniProt][1] [1]: https://w…
Answer: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This can be done via SPARQL at the UniProt.org sparql endpoint PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX fald…
Comment: KEGG Pathways
by
Sudip
• 0
No it does not. Do you know of a way that can help me achieve what I want?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
GenoMax
141k
UniRef file is 43G compressed so probably will become ~60G when uncompressed. You would likely be looking at at least that much +10-20% GB …
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