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34 results • Page
1 of 1
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0
votes
1
reply
107
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 2 hours ago by
Ram
43k • written 6 hours ago by
Nina
• 0
1
vote
1
reply
131
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 4 hours ago by
Ram
43k • written 7 hours ago by
Giorgio
• 0
0
votes
0
replies
64
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 3 hours ago by
Ram
43k • written 8 hours ago by
Bioinformatician
• 0
0
votes
1
reply
141
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 8 hours ago by
GenoMax
141k • written 9 hours ago by
rebecca.calvo
• 0
0
votes
0
replies
96
views
Using samtools with GCS (google cloud storage) on docker a docker container seems to give "Protocol Not Supported" error
samtools
gcs
9 hours ago by
abhishekghadge
• 0
0
votes
3
replies
259
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 4 hours ago by
Ram
43k • written 10 hours ago by
rheab1230
▴ 140
1
vote
4
replies
357
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 9 hours ago by
Matthias Zepper
4.5k • written 12 hours ago by
Ann
★ 2.4k
0
votes
0
replies
78
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 11 hours ago by
Ram
43k • written 13 hours ago by
mja
• 0
0
votes
0
replies
89
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
13 hours ago by
Nitin
• 0
1
vote
5
replies
391
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 10 hours ago by
GenoMax
141k • written 13 hours ago by
Luka
• 0
0
votes
0
replies
94
views
absolute path for symbolic links in Snakefile
Snakemake
updated 13 hours ago by
Ram
43k • written 13 hours ago by
yifangt86
▴ 60
0
votes
0
replies
85
views
Chemical structure validation
structure
cap
validation
metabolite
13 hours ago by
Rodolfo Adrián
• 0
2
votes
6
replies
1.0k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 13 hours ago by
GenoMax
141k • written 8 months ago by
bp22
▴ 70
0
votes
1
reply
153
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 13 hours ago by
GenoMax
141k • written 14 hours ago by
bioyas
▴ 10
0
votes
0
replies
102
views
Copy number variation plot
Copy-number-variation
genomics
updated 15 hours ago by
Ram
43k • written 15 hours ago by
Emmi
• 0
0
votes
5
replies
560
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 15 hours ago by
BioinfGuru
★ 1.7k • written 1 day ago by
rrehimi
• 0
0
votes
0
replies
90
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
15 hours ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
178
views
Could you please assist in identifying this cluster?
single-cell
updated 15 hours ago by
Ram
43k • written 16 hours ago by
Kazo
• 0
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
2
votes
7
replies
5.1k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 16 hours ago by
ATpoint
81k • written 7.1 years ago by
boymin2020
▴ 80
4
votes
11
replies
734
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 4 hours ago by
Ram
43k • written 18 hours ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
326
views
Plink merge errors.
cygwin64
bed
PLINK
19 hours ago by
Dinmukhamed
• 0
0
votes
0
replies
107
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 15 hours ago by
Ram
43k • written 19 hours ago by
Dinmukhamed
• 0
0
votes
0
replies
109
views
miRDeep2: How to get the read counts
mirdeep2
21 hours ago by
Atul K.
• 0
1
vote
2
replies
376
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
updated 22 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
rahu
• 0
0
votes
0
replies
117
views
Lncipedia GTF file error
Proteomics
updated 15 hours ago by
Ram
43k • written 23 hours ago by
atharvakarkare14
▴ 10
7
votes
3
replies
2.7k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 23 hours ago by
colindaven
6.3k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
2
replies
293
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
16 hours ago by
joe
▴ 510
0
votes
2
replies
312
views
Adding CB tag to bam file
samtools
bam
21 hours ago by
Maria
• 0
0
votes
2
replies
329
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
15 hours ago by
_quantum_girl_
▴ 10
1
vote
1
reply
330
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
14 hours ago by
renan.igor
• 0
3
votes
4
replies
435
views
Ciriquant not configuring hisat2 indexed files
ciriquant
2 hours ago by
Atul K.
• 0
5
votes
3
replies
685
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 16 hours ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 23 hours ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
34 results • Page
1 of 1
Recent Votes
Answer: MEGA Analysis Issue on High-Performance Computer
Comment: Ciriquant not configuring hisat2 indexed files
bcftools multiple commands
bcftools pipe generated file from first command with second
C: How to setup a Summarized Experiment
A: How to download genome assemblies from NCBI with a list of GCA identifiers?
what's the genomic location and name of gene responsible for orange and black patches in calico cats
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Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2
by
Ram
43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
Sorry, I see how harsh I come across. It's not good practice to use multiple versions of R in the same project. I can understand legacy pro…
Answer: MEGA Analysis Issue on High-Performance Computer
by
Mensur Dlakic
★ 27k
> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
by
GenoMax
141k
> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You c…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
rheab1230
▴ 140
I got the normalized gene count from gtex portal. they use inverse quantile normalization
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Matthias Zepper
4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Normalized how?
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
If GPT is right then it says that: > The specific gene responsible for the orange and non-orange (black or > gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Jean-Karim Heriche
27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
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