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173 results • Page
4 of 4
Sort: Votes
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0
votes
3
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726
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Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 2 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
0
replies
122
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
2 days ago by
Jacob
• 0
0
votes
0
replies
107
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
2 days ago by
fanglujing
▴ 60
0
votes
4
replies
244
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 2 days ago by
Ram
43k • written 2 days ago by
Hamtaro
▴ 50
0
votes
0
replies
105
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 days ago by
Adyasha
• 0
0
votes
4
replies
230
views
Genbank File Format
gbkformat
2 days ago by
alenew.am
• 0
0
votes
1
reply
175
views
Deseq2
Deseq2
updated 2 days ago by
Jack Tierney
▴ 360 • written 2 days ago by
Sudip
• 0
0
votes
0
replies
123
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
2 days ago by
8armed
• 0
0
votes
1
reply
272
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
2 days ago by
David Langenberger
11k
0
votes
10
replies
479
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 10 days ago by
Patadu94
• 0
0
votes
0
replies
123
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
2 days ago by
Bine
▴ 60
0
votes
3
replies
264
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 2 days ago by
GenoMax
142k • written 2 days ago by
kim
• 0
0
votes
0
replies
119
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
120
views
barcode of TCR-sequencing
barcode
2 days ago by
yueli7
▴ 250
0
votes
4
replies
250
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 2 days ago by
Michael
54k • written 2 days ago by
Riccardo
▴ 10
0
votes
0
replies
116
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 2 days ago by
Ram
43k • written 2 days ago by
Alexandros
• 0
0
votes
0
replies
148
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 2 days ago by
Ram
43k • written 2 days ago by
Chakri
• 0
0
votes
3
replies
373
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
2 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
202
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Dora
▴ 10
0
votes
1
reply
156
views
unable to get feature count results
featureCounts
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
0
votes
3
replies
259
views
KEGG Pathways
r
RNA-seq
updated 1 day ago by
Ram
43k • written 2 days ago by
Sudip
• 0
0
votes
8
replies
413
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 1 day ago by
LauferVA
4.2k • written 3 days ago by
jinyu
▴ 10
0
votes
0
replies
111
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
1 day ago by
O.rka
▴ 710
173 results • Page
4 of 4
Recent Votes
Comment: Bacterial plasmid analysis
Answer: Problem with data downloaded from Short Reads Archive (SRA)
Answer: Super ehancers
Comment: Bacterial plasmid analysis
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: What analysis suitable to identify similarly expressed genes between two samples
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Recent Replies
Answer: Loss of 'var' using concatenation of AnnData objects
by
Hugo
• 0
Similar question has been asked and answered on [scverse discourse](https://discourse.scverse.org/t/loosing-anndata-var-layer-when-using-sc…
Comment: Bacterial plasmid analysis
by
Zamin Iqbal
▴ 20
Hi Nicole. 1. The clustering will be quite different between pling and the rep types (because plasmids with one rep type can still be ve…
Comment: Do I need to go back and filter my long-reads?
by
Ram
43k
Do not delete posts that have received feedback. Engage with the user providing you feedback.
Answer: Download eQTL data of one specific gene for all tissues from GTEx
by
bk11
★ 2.4k
Please kindly check your result here. You can click `csv` and download the date in this [link][1]. **OR** If you prefer to use R, there i…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
matteo.levorato
• 0
but why not a single matrix with the 3 different condition and then by lfcShrink function get the DEGs of each condition?
Answer: Super ehancers
by
jared.andrews07
★ 16k
Sure, you can run it on them. Stitching tends to happen less frequently since the ATAC peaks are generally less wide than H3K27ac, but it'l…
Answer: What purposes can TPM values be used for?
by
jared.andrews07
★ 16k
TPMs cannot be used for intersample comparisons, but they can be used for intrasample comparisons (e.g. comparing relative expression level…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for the recommendation and the very clear explanation , it's much appreciated. I have already made core-gene phylogenies/…
Comment: What purposes can TPM values be used for?
by
Adam
▴ 30
Have you run FASTQC and checked the mapping efficiency of WT3? > would running DESeq using TPM values help solve my problem? No, DESeq sh…
Answer: How goes gene length effect the number of reads mapped
by
i.sudbery
19k
See my answer about the what hows and whens of RNA-seq normalisation here: https://www.biostars.org/p/9586553/#9586566
Comment: What purposes can TPM values be used for?
by
dsull
★ 5.9k
Since you have mutant vs wild-type, using DESeq2 is the right thing to do. Rather than showing a small table of numbers, you should make a …
Answer: What purposes can TPM values be used for?
by
i.sudbery
19k
See my post here for more details on RNA-seq normalisation: https://www.biostars.org/p/9586553/#9586566 In short, TPM normalises for ge…
Comment: Bacterial plasmid analysis
by
Zamin Iqbal
▴ 20
I vote for this, it's the best! (but also, I am Daria's PhD supervisor so I am biased). Preprint out soon(ish) [no pressure Daria!]
Comment: Downsampling long-read BAM files
by
GenoMax
142k
Is this what you used ultimately? Did this tool satisfy the "specific average depth" requirement? You could accept (green check mark) this…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
Estevão
• 0
Thank you. My budget is around 20 thousand dollars.
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