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4
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11
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763
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Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 6 hours ago by 43k • written 20 hours ago by ★ 1.7k
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 • 0
3
votes
8
replies
1.1k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 1 hour ago by 14k • written 8 months ago by ▴ 80
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 19 hours ago by 81k • written 7.1 years ago by ▴ 80
1
vote
5
replies
570
views
RNA seq differential expression analysis
RNA-seq normalization
updated 17 hours ago by ★ 1.7k • written 2 days ago by • 0
1
vote
5
replies
405
views
Duplicate marking, read names, and the SRA
SRA MarkDuplicates
updated 12 hours ago by 141k • written 15 hours ago by • 0
1
vote
4
replies
383
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 12 hours ago by 4.5k • written 14 hours ago by ★ 2.4k
3
votes
4
replies
462
views
Ciriquant not configuring hisat2 indexed files
ciriquant
4 hours ago by Atul K. • 0
0
votes
3
replies
346
views
Adding CB tag to bam file
samtools bam
updated 1 hour ago by 14k • written 1 day ago by • 0
3
votes
3
replies
322
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 1 hour ago by 14k • written 1 day ago by ▴ 510
0
votes
3
replies
286
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq gene-expression
updated 6 hours ago by 43k • written 12 hours ago by ▴ 140
5
votes
3
replies
686
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 18 hours ago by • 0 • written 9 months ago by ▴ 310
0
votes
2
replies
340
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
17 hours ago by _quantum_girl_ ▴ 10
0
votes
1
reply
84
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray HumanHT-12v4 Illumina
updated 15 minutes ago by ★ 7.0k • written 10 hours ago by • 0
1
vote
1
reply
143
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 6 hours ago by 43k • written 10 hours ago by • 0
0
votes
1
reply
138
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie Cufflinks Ballgown DESeq2
updated 4 hours ago by 43k • written 8 hours ago by • 0
0
votes
1
reply
159
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun metagenomics blastp taxonomy
updated 10 hours ago by 141k • written 12 hours ago by • 0
1
vote
1
reply
339
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
16 hours ago by renan.igor • 0
1
vote
1
reply
330
views
Plink merge errors.
cygwin64 bed PLINK
21 hours ago by Dinmukhamed • 0
0
votes
1
reply
163
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 15 hours ago by 141k • written 16 hours ago by ▴ 10
0
votes
1
reply
189
views
Could you please assist in identifying this cluster?
single-cell
updated 17 hours ago by 43k • written 18 hours ago by • 0
0
votes
0
replies
97
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
15 hours ago by Nitin • 0
0
votes
0
replies
97
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
18 hours ago by DanielEB_fisk ▴ 20
0
votes
0
replies
116
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 17 hours ago by 43k • written 21 hours ago by • 0
0
votes
0
replies
126
views
Lncipedia GTF file error
Proteomics
updated 17 hours ago by 43k • written 1 day ago by ▴ 10
0
votes
0
replies
111
views
Copy number variation plot
Copy-number-variation genomics
updated 17 hours ago by 43k • written 17 hours ago by • 0
0
votes
0
replies
93
views
Chemical structure validation
structure cap validation metabolite
16 hours ago by Rodolfo Adrián • 0
0
votes
0
replies
104
views
absolute path for symbolic links in Snakefile
Snakemake
updated 15 hours ago by 43k • written 15 hours ago by ▴ 60
0
votes
0
replies
117
views
miRDeep2: How to get the read counts
mirdeep2
23 hours ago by Atul K. • 0
0
votes
0
replies
90
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 13 hours ago by 43k • written 15 hours ago by • 0
0
votes
0
replies
106
views
Using samtools with GCS (google cloud storage) on docker a docker container seems to give "Protocol Not Supported" error
samtools gcs
12 hours ago by abhishekghadge • 0
1
vote
0
replies
50
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
1 hour ago by mathavanbioinfo ▴ 90
32 results • Page 1 of 1
Recent Votes
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Answer: Cellranger count error: Input FASTQ file ended prematurely
Answer: RNA seq differential expression analysis
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
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Recent Replies
Answer: Removing Illumina microarray probes with no expression HumanHT-12v4 by Gordon Smyth ★ 7.0k
Type ``` help("read.idat") ``` and read the example at the bottom of the page, which shows you how to set the `other$Detection` component o…
Comment: Free/open source 23andme-like analysis by swbarnes2 14k
Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely by swbarnes2 14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
Comment: Cellranger count error: Input FASTQ file ended prematurely by ATpoint 81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file by swbarnes2 14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
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…
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