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249 results • Page
1 of 5
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76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
7 hours ago by
Kevin Blighe
87k
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 6 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
0
votes
14
replies
3.4k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 20 hours ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
3
votes
13
replies
634
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 17 hours ago by
bk11
★ 2.3k • written 7 weeks ago by
Sofia
• 0
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 4 days ago by
ATpoint
82k • written 5 days ago by
BioinfGuru
★ 1.7k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 6 days ago by
kjngo
• 0 • written 12.0 years ago by
Gabriel R.
★ 2.9k
11
votes
12
replies
936
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 6 days ago by
Ram
43k • written 6 days ago by
iamsmor
• 0
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 1 day ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
4
votes
11
replies
479
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 1 day ago by
LauferVA
4.2k • written 2 days ago by
dominickd
• 0
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
1
vote
10
replies
856
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
13 hours ago by
DKA
▴ 40
0
votes
10
replies
369
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
2
votes
10
replies
723
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 6 days ago by
GenoMax
141k • written 7 days ago by
me
• 0
3
votes
9
replies
388
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 20 hours ago by
Istvan Albert
100k • written 2 days ago by
Κοσμάς
• 0
2
votes
9
replies
800
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 6 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
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
3
votes
9
replies
785
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 6 days ago by
Elisabeth Gasteiger
★ 2.4k • written 7 days ago by
Jacky
• 0
0
votes
8
replies
281
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 0
3
votes
8
replies
408
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 4 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
1
vote
8
replies
672
views
Adding CB tag to bam file
samtools
bam
updated 1 hour ago by
Pierre Lindenbaum
161k • written 6 days ago by
Maria
• 0
3
votes
8
replies
1.2k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 5 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 6 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 6 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 5 days ago by
ATpoint
82k • written 7.1 years ago by
boymin2020
▴ 80
2
votes
7
replies
805
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 7 days ago by
quentinperriere
• 0
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 4.0 years ago by
Ankit
▴ 500
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 6 days ago by
Ram
43k • written 4.9 years ago by
borkk
▴ 140
4
votes
7
replies
327
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 54 minutes ago by
dsull
★ 5.8k • written 1 day ago by
VITALA
• 0
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 6 days ago by
colindaven
6.4k • written 10.9 years ago by
Ontheway
▴ 10
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 6 days ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
7
votes
6
replies
450
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
3 days ago by
analyst
▴ 30
0
votes
6
replies
423
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 23 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
3
votes
6
replies
627
views
Ciriquant not configuring hisat2 indexed files
ciriquant
3 days ago by
Atul K.
• 0
0
votes
6
replies
282
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
1 day ago by
Sd
• 0
8
votes
5
replies
5.0k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
1
vote
5
replies
244
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 4 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
1
vote
5
replies
298
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
1 day ago by
anasjamshed
▴ 120
1
vote
5
replies
550
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 5 days ago by
GenoMax
141k • written 5 days ago by
Luka
• 0
1
vote
5
replies
687
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 5 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
rrehimi
• 0
3
votes
5
replies
241
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 2 days ago by
GenoMax
141k • written 3 days ago by
ahmad.sajad4541
• 0
2
votes
5
replies
428
views
Marking duplicates using UMIs
Deduplication
UMI
updated 2 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
1
vote
5
replies
585
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 1 day ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 3 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
2
votes
5
replies
508
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 4 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
Giorgio
• 0
0
votes
5
replies
273
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
22 hours ago by
njornet
▴ 20
3
votes
5
replies
532
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
3 days ago by
n_navy
• 0
2
votes
5
replies
676
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
249 results • Page
1 of 5
Recent Votes
Answer: Fetch table from clinvar database according to a list of rsid
Comment: Fetch table from clinvar database according to a list of rsid
Comment: Adding CB tag to bam file
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
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Recent Replies
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
b.contreras.moreira
▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM
by
VITALA
• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result
by
ahmad.sajad4541
• 0
Thank you so much. Should i proceed for annotation step?
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