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35 results • Page
1 of 1
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0
votes
2
replies
50
views
Limma returned only positive logFC values
edgeR
differential-expression
deg
limma
23 minutes ago by
melissachua90
▴ 40
0
votes
0
replies
21
views
Alternative approach to rarefying in 16S rRNA analysis
16S
Rarefying
rRNA
2 hours ago by
zhangdengwei
▴ 180
0
votes
0
replies
17
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
updated 2 hours ago by
GenoMax
129k • written 2 hours ago by
tahsinkhan570
• 0
0
votes
3
replies
102
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 1 hour ago by
GenoMax
129k • written 3 hours ago by
ev97
• 0
0
votes
1
reply
50
views
Gene enrichment analysis with GOfuncR
R
GOfuncR
gene-enrichment-analysis
updated 2 hours ago by
jv
★ 1.2k • written 3 hours ago by
Eliza
• 0
0
votes
0
replies
54
views
Which is the minor allele in ped file in plink?
plink
updated 4 hours ago by
GenoMax
129k • written 4 hours ago by
khn
▴ 130
0
votes
0
replies
41
views
Correct way to remove Nextera adapters from ITS sequences
adapters
ITS
trimmomatic
5 hours ago by
mattze731
▴ 10
0
votes
0
replies
50
views
What statistical test should I use to analyse my two set of transcriptomique data?
transcriptome
6 hours ago by
F.Bedjou
▴ 10
0
votes
0
replies
44
views
Difference MITOS WebServer and MITOS 2 Webserver
MITOS2
WebServer
Difference
MITOS
8 hours ago by
hashim.rana11
▴ 20
0
votes
0
replies
76
views
Integrate RDS files
integration
16 hours ago by
Andy
▴ 50
0
votes
1
reply
115
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 18 hours ago by
Ram
39k • written 20 hours ago by
akainth
▴ 10
1
vote
9
replies
244
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 18 hours ago by
Ram
39k • written 21 hours ago by
peavy
• 0
0
votes
1
reply
344
views
How to quantification proteomics data
proteomics
updated 20 hours ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
1
vote
4
replies
184
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
20 hours ago by
Daniel
▴ 30
0
votes
2
replies
1.3k
views
How to perform statistical analysis of label free experiment using results from Proteome Discoverer?
Proteome-Discoverer
Label-Free
Proteomics
updated 22 hours ago by
Ram
39k • written 4.5 years ago by
k2bhide
▴ 80
0
votes
0
replies
65
views
Label free quantification in Proteome discoverer software
proteomics
quantification
spectrometry
shotgun
23 hours ago by
eqoa45
• 0
0
votes
1
reply
128
views
CHiP-Seq Questions
DiffBind
CHiP-Seq
updated 23 hours ago by
jared.andrews07
★ 14k • written 1 day ago by
B.N.
• 0
1
vote
2
replies
137
views
hisat2 Error 137
hisat2
RNA-seq
22 hours ago by
Forough
▴ 10
2
votes
5
replies
253
views
Embryo transcriptome
database
transcriptome
SRA
updated 18 hours ago by
ATpoint
72k • written 1 day ago by
firefox91
• 0
0
votes
6
replies
283
views
variant allelic fraction
vep
updated 1 hour ago by
Ram
39k • written 1 day ago by
Jom
• 0
0
votes
1
reply
163
views
Differential protein expression analysis
R
proteomic
statistics
updated 5 hours ago by
dsull
★ 4.2k • written 2 days ago by
Ribo
▴ 40
0
votes
2
replies
230
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
20 hours ago by
demoraesdiogo2017
▴ 90
2
votes
2
replies
182
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
analysis
CD
Protocol
updated 24 minutes ago by
Ram
39k • written 5 days ago by
linnet.roque6
▴ 10
0
votes
2
replies
274
views
too many zeros in 16S rRNA amplicon sequencing data
16S
rRNA
2 hours ago by
zhangdengwei
▴ 180
0
votes
0
replies
364
views
How to compile Java files in bash?
Bash
Java
updated 28 minutes ago by
Ram
39k • written 18 months ago by
ezraamustafa3
• 0
0
votes
2
replies
768
views
Error in mvnX when running processSamples.R of OncoCNV
variant-calling
oncocnv
cnv
updated 17 minutes ago by
Ram
39k • written 3.5 years ago by
mwarrier
• 0
2
votes
6
replies
645
views
How to identify the corresponding gene of a short sequence of a genome?
fasta
gene
genome
sequence
updated 29 minutes ago by
Ram
39k • written 3.5 years ago by
Kumar
▴ 100
0
votes
8
replies
1.5k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython
python
updated 1 hour ago by
Ram
39k • written 3.5 years ago by
muhammad.khizerkiet
• 0
1
vote
3
replies
1.4k
views
Is there any tool available for sequence alignment concatenation and supermatrix file generation other than Fastconcat-G?
Assembly
alignment
software-error
updated 19 hours ago by
Ram
39k • written 3.6 years ago by
Kumar
▴ 100
2
votes
4
replies
822
views
Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python
biopython
updated 21 hours ago by
Ram
39k • written 3.6 years ago by
Christian
• 0
1
vote
2
replies
521
views
How to mine plant-inducible promoter (PIP) box from Xanthomonas genus genome?
assembly
gene
genome
next-gen
updated 21 hours ago by
Ram
39k • written 3.6 years ago by
Kumar
▴ 100
0
votes
0
replies
1.1k
views
Assembly error on Ipyrad step 3: ERROR IPyradError(None)
rad-seq
ipyrad
updated 21 hours ago by
Ram
39k • written 3.6 years ago by
mgpastos
▴ 10
0
votes
0
replies
606
views
Pan-genome Bioinformatics Workshops?
pan-genome
workshop
updated 22 hours ago by
Ram
39k • written 3.7 years ago by
cassondranewman
• 0
0
votes
2
replies
1.0k
views
Find most upregulated genes in one library?
EdgeR
RNA-Seq
Rsubread
updated 22 hours ago by
Ram
39k • written 3.7 years ago by
williams.damon26
▴ 10
0
votes
4
replies
5.0k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 18 hours ago by
Franco
• 0 • written 5.6 years ago by
ac.research
▴ 30
35 results • Page
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Answer: Contigs to chromosomes annotation
Bioinformatics in drug designing
Tagsnps: Is There An Easy Way To Select Tagsnps From The 1000 Genomes Project?
Measure Tag Snps, R Package, Tools
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Answer: [Meta] Use of AI
Download all Becteria and protist fasta protein sequences from UNIPROT proteomes
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Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Several hundred to 10000 DEGs. Would normalization affect logFC?
Answer: Contigs to chromosomes annotation
by
Darked89
4.3k
Not sure if it is the easiest, but you can map your new assembly to i.e. Dmel genome using LAST: * www: https://gitlab.com/mcfrith/last …
Answer: Gene prediction software
by
Darked89
4.3k
How complete/polished is your catfish genome assembly? Also: do you have some good quality RNA-Seq? With a draft genome it would be…
Comment: Limma returned only positive logFC values
by
LChart
2.6k
It'd be helpful to know how many differentially expressed genes there are. If you've got a handful and they're all upregulated, I wouldn't …
Comment: variant allelic fraction
by
Ram
39k
Cross-posted on bioinfo SE: https://bioinformatics.stackexchange.com/questions/21118/how-to-calculate-the-variant-allelic-fraction-vaf OP,…
Comment: Gene enrichment analysis with GOfuncR
by
jv
★ 1.2k
how is this post different from your previous post? <https://www.biostars.org/p/9565445/#9565445>
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
by
GenoMax
129k
You can `cat` the respective R1/R2 files in same order e.g. `cat Run1_R1.fq.gz Run2_R1.fq.gz > R1.fq.gz`.
Comment: too many zeros in 16S rRNA amplicon sequencing data
by
zhangdengwei
▴ 180
Exactly. I agree that this is due to the NovaSeq which is not very compatible with qimme2 DADA2 pipeline. I finally surrendered to other ap…
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
by
ev97
• 0
Thanks for your quick reply! How would you merge them?
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
by
Trivas
★ 1.2k
My guess is that some samples were resequenced. I'd recommend just merging the respective R1 and R2s and treat them as one sample.
Comment: Get protein information from ensemblbacteria using interpro
by
sgiorgetti
▴ 10
@GenoMax Apologies for my belated reply. Agreed, the REST endpoint above supports Ensembl IDs only. Mentioned because both the initial que…
Comment: VEP tab/vcf - Different output
by
Ben_Ensembl
★ 2.2k
Ah, I see. Then, no, I don't believe that this is possible with the VEP
Comment: VEP tab/vcf - Different output
by
Jeremy Leipzig
21k
I don't think that is in VCF-style coordinates which show deletions like chr1:99:AG -> A instead of chr1:100:G -> -
Comment: Help with running ATAC using Encode pipeline
by
Chris
▴ 100
Sure, here is my json file, I have 8 fastq files: { "atac.title" : “atac)”, "atac.description" : “Encode”, …
Comment: Differential protein expression analysis
by
dsull
★ 4.2k
Yes, you need to log-transform. I've had a good experience using limma for proteomics analyses (limma uses a moderated t-test).
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