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Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 20 minutes ago by 81k • written 1 day ago by ★ 1.7k
3
votes
8
replies
1.1k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 6 hours 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 23 hours ago by 81k • written 7.1 years ago by ▴ 80
1
vote
5
replies
421
views
Duplicate marking, read names, and the SRA
SRA MarkDuplicates
updated 17 hours ago by 141k • written 20 hours ago by • 0
1
vote
5
replies
583
views
RNA seq differential expression analysis
RNA-seq normalization
updated 22 hours ago by ★ 1.7k • written 2 days ago by • 0
0
votes
5
replies
5.8k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 2 hours ago by • 0 • written 6.5 years ago by ▴ 30
3
votes
4
replies
471
views
Ciriquant not configuring hisat2 indexed files
ciriquant
9 hours ago by Atul K. • 0
1
vote
4
replies
404
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 16 hours ago by 4.5k • written 19 hours ago by ★ 2.4k
5
votes
3
replies
687
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 23 hours ago by • 0 • written 9 months ago by ▴ 310
0
votes
3
replies
312
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq gene-expression
updated 10 hours ago by 43k • written 17 hours ago by ▴ 140
0
votes
3
replies
379
views
Adding CB tag to bam file
samtools bam
updated 6 hours ago by 14k • written 1 day ago by • 0
3
votes
3
replies
353
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 6 hours ago by 14k • written 1 day ago by ▴ 510
0
votes
2
replies
349
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
22 hours ago by _quantum_girl_ ▴ 10
0
votes
2
replies
30
views
bam merging for archaic samples
samtools bam ancient merge
37 minutes ago by Matteo Ungaro ▴ 100
0
votes
1
reply
40
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
updated 1 hour ago by 161k • written 4 hours ago by ▴ 20
0
votes
1
reply
121
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray HumanHT-12v4 Illumina
updated 4 hours ago by ★ 7.0k • written 15 hours ago by • 0
0
votes
1
reply
199
views
Could you please assist in identifying this cluster?
single-cell
updated 22 hours ago by 43k • written 23 hours ago by • 0
1
vote
1
reply
339
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
21 hours ago by renan.igor • 0
0
votes
1
reply
162
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie Cufflinks Ballgown DESeq2
updated 9 hours ago by 43k • written 13 hours ago by • 0
0
votes
1
reply
175
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun metagenomics blastp taxonomy
updated 15 hours ago by 141k • written 16 hours ago by • 0
0
votes
1
reply
172
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 20 hours ago by 141k • written 21 hours ago by ▴ 10
1
vote
1
reply
157
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 10 hours ago by 43k • written 14 hours ago by • 0
0
votes
0
replies
123
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 22 hours ago by 43k • written 1 day ago by • 0
0
votes
0
replies
104
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
19 hours ago by Nitin • 0
0
votes
0
replies
101
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 18 hours ago by 43k • written 20 hours ago by • 0
0
votes
0
replies
119
views
Copy number variation plot
Copy-number-variation genomics
updated 21 hours ago by 43k • written 22 hours ago by • 0
0
votes
0
replies
131
views
Lncipedia GTF file error
Proteomics
updated 21 hours ago by 43k • written 1 day ago by ▴ 10
0
votes
0
replies
114
views
Using samtools with GCS (google cloud storage) on docker a docker container seems to give "Protocol Not Supported" error
samtools gcs
16 hours ago by abhishekghadge • 0
0
votes
0
replies
110
views
absolute path for symbolic links in Snakefile
Snakemake
updated 20 hours ago by 43k • written 20 hours ago by ▴ 60
1
vote
0
replies
132
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
6 hours ago by mathavanbioinfo ▴ 90
0
votes
0
replies
103
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
22 hours ago by DanielEB_fisk ▴ 20
0
votes
0
replies
100
views
Chemical structure validation
structure cap validation metabolite
20 hours ago by Rodolfo Adrián • 0
32 results • Page 1 of 1
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Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
Answer: Ubuntu storage space is decreasing automatically
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
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
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Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by ATpoint 81k
You can, if you use RStudio via Docker, for example `bioconductor/bioconductor_docker`. I currently manage many different projects with thi…
Comment: bam merging for archaic samples by Matteo Ungaro ▴ 100
@Pierre Lindenbaum I see. So, I can actually manipulate just one single RG tag at the time with `samtools`? Which flag should I use, or sho…
Comment: bam merging for archaic samples by Pierre Lindenbaum 161k
RG tag "L9302" is missing the the BAM header. You should have something like this in the BAM header ``` @RG ID:L9302 SM:L9302 ``` may be…
Answer: Filtering sam or bam file with maximum matching region by Pierre Lindenbaum 161k
> . Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to? samtools depth i…
Comment: Calculate Radius of Gyration [python 3] by ndm1096 • 0
Hello Franco. I am very much new with bioinformatics but I have been tasked with studying the radius of gyration of a timeseries of a prote…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
That makes a lot more sense. Thank you.
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…
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