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213 results • Page
3 of 5
Sort: replies
Rank
Views
Votes
Replies
4
votes
2
replies
221
views
Execute R command on specific termimal
R
updated 1 day ago by
Ram
41k • written 2 days ago by
QX
• 0
3
votes
2
replies
182
views
Can't do runPCA after merging a splited Seurat object before UMAP
scRNA-seq
Seurat
1 day ago by
wanaga3166
▴ 10
5
votes
2
replies
4.4k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
6 days ago by
GenoMax
136k
0
votes
2
replies
197
views
Very low successfully assigned alignments with feature counts
featureCounts
RNA-seq
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
Manuel
• 0
0
votes
2
replies
271
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
updated 3 days ago by
Ram
41k • written 10 days ago by
DareDevil
★ 3.3k
4
votes
2
replies
276
views
Ambient RNA removal method that generates whole (integer) counts
pseudobulk
soupX
DESeq2
single-cell
1 day ago by
EK
• 0
2
votes
2
replies
222
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
3 days ago by
hkarakurt
▴ 180
3
votes
2
replies
252
views
RNA-seq log2 fold change to linear
RNA-seq
DGE
updated 3 days ago by
jared.andrews07
★ 16k • written 4 days ago by
hmiller
• 0
0
votes
2
replies
223
views
Downsampling ATAC-seq BAM files
ATAC-seq
2 days ago by
Elise
• 0
0
votes
2
replies
657
views
Regarding Error query in publically available RNA seq analysis by R studio
GEO
Rstudio
RNA-seq
NGS
updated 2 days ago by
Ram
41k • written 2.2 years ago by
ruddhida
• 0
0
votes
2
replies
142
views
Opinion on miRNA pipeline
miRNA
pipeline
4 hours ago by
ju_ra
• 0
4
votes
2
replies
276
views
KEGG DATABASE
DATABASE
KEGG
updated 2 days ago by
jv
★ 1.3k • written 5 days ago by
Sijjil
• 0
0
votes
2
replies
106
views
Where to download excel file to include major human disease, prevalence and incidence?
Disease
Burden
updated 3 hours ago by
GenoMax
136k • written 6 hours ago by
Shicheng Guo
★ 9.3k
5
votes
2
replies
267
views
Fastest way to convert BED to GTF/GFF with gene_ids?
gff
convert
bed
gtf
updated 5 days ago by
cmdcolin
★ 3.4k • written 5 days ago by
alejandrogzi
▴ 110
0
votes
1
reply
144
views
Microbial gene coverage from blast result
gene
coverage
3 days ago by
aanchal.yadav
• 0
0
votes
1
reply
151
views
Issues with Chromosome Encoding and VCF Annotation in dbSNP Alpha Release
bcftools
dbSNP
tabix
vcf
updated 2 days ago by
Ram
41k • written 3 days ago by
Fernando
• 0
1
vote
1
reply
1.1k
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 2 days ago by
charles.feigin
• 0 • written 7 weeks ago by
xinrantian
▴ 20
2
votes
1
reply
258
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools
softclip
updated 4 days ago by
aw7
▴ 230 • written 7 days ago by
ManuelDB
▴ 80
0
votes
1
reply
259
views
vg: How to find node Position and source(sample) ?
vg
updated 4 days ago by
colindaven
5.8k • written 9 days ago by
zhang yi xing
▴ 20
1
vote
1
reply
131
views
Process Truncated fastq file
fastqc
fastq
updated 4 days ago by
GenoMax
136k • written 4 days ago by
waqaskhokhar999
▴ 150
1
vote
1
reply
133
views
locuszoom error
locuszoom
updated 4 days ago by
GenoMax
136k • written 4 days ago by
nanodano
▴ 30
1
vote
1
reply
213
views
How to use Nextflow to call scripts from different environments?
anaconda
conda
nextflow
updated 1 day ago by
Ram
41k • written 2 days ago by
O.rka
▴ 710
0
votes
1
reply
165
views
Cell ranger multi for demultiplexing FB files and GEX files
cellranger
updated 1 day ago by
Ram
41k • written 2 days ago by
Shloka
• 0
0
votes
1
reply
177
views
using RMA normalized microarray in Limma
GEOdatabase
Microarray
limma
RMA
updated 4 days ago by
ATpoint
78k • written 5 days ago by
fluke
• 0
0
votes
1
reply
160
views
How to remove 3rd codon positions in a multiple sequence allignment?
i
updated 2 days ago by
Ram
41k • written 3 days ago by
francesco.degiglio
• 0
3
votes
1
reply
152
views
GEO dataset Microarray data analysis help
R
microarray
NCBI
GEO
updated 2 days ago by
Ram
41k • written 3 days ago by
Confused_human
▴ 20
0
votes
1
reply
227
views
How to convert UNITE dataset into ecoPCR format to perform insilico PCR?
obiconvert
ecoPCR
updated 3 days ago by
vinranke-adel0j
• 0 • written 7 weeks ago by
shristymaurya012
• 0
0
votes
1
reply
179
views
Contrasts in R
contrasts
r
updated 2 days ago by
jv
★ 1.3k • written 2 days ago by
SGMS
▴ 130
0
votes
1
reply
331
views
News:
RNA-Seq Data Analysis Workshop (March 11 - 14, 2024 in Berlin, Germany)
NGS
RNA-Seq
Workshop
1 day ago by
David Langenberger
10k
0
votes
1
reply
143
views
absolute running error: Error in if (!is.na(res)) { : the condition has length > 1
ABSOLUTE
error
1 day ago by
qiuting
• 0
0
votes
1
reply
580
views
How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
MLST
phylogenetic
nanopre
updated 3 days ago by
Joe
21k • written 3 days ago by
Ralph
• 0
0
votes
1
reply
394
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
updated 6 days ago by
Jordan M Eizenga
▴ 410 • written 13 days ago by
Wenke
• 0
0
votes
1
reply
512
views
Problems separating and converting molecule files with openbabel
openbabel
updated 3 days ago by
mthm
▴ 50 • written 16 months ago by
smithk
• 0
0
votes
1
reply
206
views
Dimensionality reduction on data sets with variable dimensions
PCA
dimensionality_reduction
RNA_secondary_structure
updated 5 days ago by
Mensur Dlakic
★ 25k • written 5 days ago by
rtrende
▴ 80
0
votes
1
reply
178
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind
ChIP-seq
updated 23 hours ago by
Rory Stark
★ 2.0k • written 8 days ago by
DINESHR
• 0
1
vote
1
reply
366
views
Trinity 'genes' too much
Trinity
RNA-seq
updated 2 days ago by
Ram
41k • written 2.1 years ago by
Hou
• 0
1
vote
1
reply
289
views
Forum:
want to work in open source project/project in bioinformatics
project
updated 3 days ago by
Ram
41k • written 12 days ago by
Afeef
• 0
0
votes
1
reply
484
views
FASTQ files for 30x 1KGP of Phase 3 data
1000genomes
fastq
updated 21 hours ago by
Ram
41k • written 13 months ago by
Qboy
• 0
0
votes
1
reply
216
views
Issue with genetic QC sex check
plink
6 days ago by
kl
▴ 10
0
votes
1
reply
105
views
Does orthofinder allow more than one proteome per species as input ?
comparative-genomics
orthology
updated 21 hours ago by
Ram
41k • written 23 hours ago by
Sara
• 0
0
votes
1
reply
142
views
scRNA data analysis , how to compare pattern in multiple samples
R
scRNA
updated 21 hours ago by
Ram
41k • written 1 day ago by
Confused_human
▴ 20
0
votes
1
reply
690
views
Alternative tool for split'N'trim
SNP
Galaxy
Single-cell
RNA-seq
updated 2 days ago by
Ram
41k • written 3.6 years ago by
aiswaryabioinfo
▴ 30
0
votes
1
reply
171
views
AssemblyMAFFromAnchorWavePlugin IndexOutOfBoundsException
phg
updated 2 days ago by
lcj34
▴ 250 • written 2 days ago by
ryan
• 0
1
vote
1
reply
112
views
recommend gene ranking methods when doing GSEA
Gene_rank
GSEA
updated 19 hours ago by
rpolicastro
12k • written 22 hours ago by
luckyday1661
• 0
0
votes
1
reply
141
views
News:
Course: Genome Assembly and Annotation
Biodiversity
Genome-Assembly
Genome-Annotation
Long-reads
updated 3 days ago by
Ram
41k • written 7 days ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
1.3k
views
Correlation RNA-seq and ATAC-seq
RNA-Seq
R
gene
updated 2 days ago by
Tao Zhu
▴ 10 • written 3.4 years ago by
pastel950818
• 0
1
vote
1
reply
158
views
ANNOVAR Download Failing
ANNOVAR
updated 2 days ago by
Ram
41k • written 2 days ago by
tony
• 0
0
votes
1
reply
111
views
get gene name from rsID
dbSNP
updated 16 hours ago by
Ram
41k • written 18 hours ago by
a3532321
• 0
0
votes
1
reply
211
views
doubt about usage of megahit
trinity
megahit
updated 6 days ago by
Istvan Albert
99k • written 7 days ago by
meera
• 0
0
votes
1
reply
165
views
Sorted bam files are empty after sorting them from bam
bam
dna
updated 2 days ago by
Ram
41k • written 2 days ago by
mgranada3
▴ 30
213 results • Page
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Recent Votes
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: Issue softclipping reads when they belong and don't belong to a common amplicon
Answer: how to remove multiple columns from a file in R
Answer: how to remove multiple columns from a file in R
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Recent Replies
Comment: Differential expression using Bowtie2
by
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78k
> What would you do if you wanted to compare differential expression of a gene across tissues from RNA-seq data? Get a dataset that has ev…
Comment: How to query 1000 genomes project VCF files for specific regions without downloa
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kilojarek
▴ 10
Thanks @Pierre this is great to know, although it doesn't solve my issue of this being R-self-contained. rsamtools doesn't seem to carry fu…
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8d8fc19e
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Ok, thanks for letting me know. What would you do if you wanted to compare differential expression of a gene across tissues from RNA-seq da…
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To put it more simply with another example, I try to display every possible order for every phyla founded in my run but I don't find the l…
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marie.harmel
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Thank you for your answer but unfortunately I tried it and it makes the same kind of ouptut as mine, with multtiple new (false) lines (spl…
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78k
What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
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Dear [Brian][1] I realized that problem is with callvariants.sh script because when I called variants using freebayes I did not find aforem…
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
by
analyst
▴ 10
Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
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Since all your sequences have the same length (say M) and you are only looking concerned with hamming distance you can encode your sequence…
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136k
ChatGPT says Disease Prevalence Approximate Number of Cases (Worldwide) Cardiovascular Diseases High Over 17 million deaths annual…
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Thank you very much! I see you decided to go for Bowtie as aligner. Do you see any issue in using STAR (as a splice aware reader technicall…
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Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
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again, it's a problem with the variant caller, which is ?
Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
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Not only opposite case but same case nucleotides are also present in vcf fle. ![enter image description here][1] [1]: /media/images/4…
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