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29 results • Page
1 of 1
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Votes
Replies
0
votes
2
replies
48
views
bam merging for archaic samples
samtools
bam
ancient
merge
1 hour ago by
Matteo Ungaro
▴ 100
0
votes
1
reply
55
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
updated 3 hours ago by
Pierre Lindenbaum
161k • written 5 hours ago by
analyst
▴ 20
0
votes
1
reply
128
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 5 hours ago by
Gordon Smyth
★ 7.0k • written 16 hours ago by
Bioinformatician
• 0
1
vote
0
replies
151
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
7 hours ago by
mathavanbioinfo
▴ 90
0
votes
1
reply
173
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 10 hours ago by
Ram
43k • written 14 hours ago by
Nina
• 0
1
vote
1
reply
160
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 12 hours ago by
Ram
43k • written 16 hours ago by
Giorgio
• 0
0
votes
1
reply
179
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 16 hours ago by
GenoMax
141k • written 18 hours ago by
rebecca.calvo
• 0
0
votes
0
replies
116
views
Using samtools with GCS (google cloud storage) on docker a docker container seems to give "Protocol Not Supported" error
samtools
gcs
17 hours ago by
abhishekghadge
• 0
0
votes
3
replies
316
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 12 hours ago by
Ram
43k • written 18 hours ago by
rheab1230
▴ 140
1
vote
4
replies
412
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 17 hours ago by
Matthias Zepper
4.5k • written 20 hours ago by
Ann
★ 2.4k
0
votes
0
replies
103
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 19 hours ago by
Ram
43k • written 21 hours ago by
mja
• 0
0
votes
0
replies
106
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
21 hours ago by
Nitin
• 0
1
vote
5
replies
423
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 18 hours ago by
GenoMax
141k • written 21 hours ago by
Luka
• 0
0
votes
0
replies
112
views
absolute path for symbolic links in Snakefile
Snakemake
updated 21 hours ago by
Ram
43k • written 21 hours ago by
yifangt86
▴ 60
0
votes
0
replies
103
views
Chemical structure validation
structure
cap
validation
metabolite
21 hours ago by
Rodolfo Adrián
• 0
3
votes
8
replies
1.1k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 7 hours ago by
swbarnes2
14k • written 8 months ago by
bp22
▴ 80
0
votes
1
reply
174
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 21 hours ago by
GenoMax
141k • written 22 hours ago by
bioyas
▴ 10
0
votes
0
replies
120
views
Copy number variation plot
Copy-number-variation
genomics
updated 23 hours ago by
Ram
43k • written 23 hours ago by
Emmi
• 0
1
vote
5
replies
587
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 23 hours ago by
BioinfGuru
★ 1.7k • written 2 days ago by
rrehimi
• 0
0
votes
1
reply
201
views
Could you please assist in identifying this cluster?
single-cell
updated 23 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
5
votes
13
replies
831
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 1 hour ago by
ATpoint
81k • written 1 day ago by
BioinfGuru
★ 1.7k
0
votes
0
replies
125
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 23 hours ago by
Ram
43k • written 1 day ago by
Dinmukhamed
• 0
0
votes
0
replies
132
views
Lncipedia GTF file error
Proteomics
updated 23 hours ago by
Ram
43k • written 1 day ago by
atharvakarkare14
▴ 10
3
votes
3
replies
357
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 7 hours ago by
swbarnes2
14k • written 1 day ago by
joe
▴ 510
0
votes
3
replies
384
views
Adding CB tag to bam file
samtools
bam
updated 7 hours ago by
swbarnes2
14k • written 1 day ago by
Maria
• 0
0
votes
2
replies
350
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
23 hours ago by
_quantum_girl_
▴ 10
1
vote
1
reply
340
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
22 hours ago by
renan.igor
• 0
3
votes
4
replies
472
views
Ciriquant not configuring hisat2 indexed files
ciriquant
10 hours ago by
Atul K.
• 0
0
votes
5
replies
5.8k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 3 hours ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
29 results • Page
1 of 1
Recent Votes
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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