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110,335 results • Page
1 of 2207
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Votes
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0
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2
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499
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ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 15 minutes ago by
Ram
39k • written 12 months ago by
Meeran
• 0
0
votes
3
replies
312
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 1 hour ago by
Zhenyu Zhang
▴ 800 • written 3 days ago by
Camilo Andres
▴ 30
0
votes
2
replies
25
views
gatk Hardfilter Error
hardfilter
updated 1 hour ago by
Pierre Lindenbaum
154k • written 1 hour ago by
bestone
▴ 10
0
votes
2
replies
41
views
How to make a dotplot for bulk RNA average expression ?
Dotplot
RNA-seq
1 hour ago by
LionisOne
• 0
0
votes
1
reply
31
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 2 hours ago by
andres.firrincieli
3.3k • written 2 hours ago by
kamanovae
▴ 80
0
votes
0
replies
26
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 2 hours ago by
Ram
39k • written 2 hours ago by
fafad046
• 0
743
votes
162
replies
113k
views
101 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 weeks ago by
Biostar
1.8k • written 6.5 years ago by
Istvan Albert
98k
1
vote
3
replies
55
views
Salmon Index
transcriptomics
Bulk
RNA-sequencing
updated 42 minutes ago by
GenoMax
129k • written 2 hours ago by
ashleymb1116
• 0
1
vote
4
replies
493
views
Expected number of haplotype IDs per path in PHG
PHG
updated 3 hours ago by
Ram
39k • written 5 weeks ago by
twrl8
• 0
0
votes
6
replies
205
views
how to create correlation matrix R
pearson-correlation
R
updated 4 hours ago by
GenoMax
129k • written 10 hours ago by
satva72
• 0
0
votes
1
reply
50
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
updated 4 hours ago by
GenoMax
129k • written 4 hours ago by
Mohd
• 0
0
votes
1
reply
58
views
sorting BAM file
BAM
updated 3 hours ago by
Ram
39k • written 4 hours ago by
Mohammad Amin
• 0
0
votes
1
reply
52
views
Search SRA metadata for Histological_Type and Body_Site
sra
updated 4 hours ago by
GenoMax
129k • written 5 hours ago by
oakhamwolf
▴ 20
0
votes
3
replies
137
views
NCBI refseq ids to uniprot ids
proteinIds
Uniprot
updated 4 hours ago by
Jiyao Wang
▴ 310 • written 8 hours ago by
t.ali
• 0
1
vote
3
replies
96
views
Covert multiple short sequence into list of IUPAC motif
sequence
updated 4 hours ago by
GenoMax
129k • written 6 hours ago by
praasu
▴ 40
0
votes
0
replies
41
views
Resequencing data of pangenome
NGS
PanGenome
Resequence
data
7 hours ago by
bioinfo223
• 0
1
vote
2
replies
120
views
Graphing Average Expression of Group of Genes
Boxplot
R
updated 3 hours ago by
Shred
★ 1.2k • written 12 hours ago by
cthangav
▴ 40
0
votes
0
replies
39
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 7 hours ago by
zx8754
11k • written 7 hours ago by
sidrah.maryam
▴ 50
0
votes
0
replies
46
views
Seurat: How to get all genes name of a cell ?
seurat
updated 3 hours ago by
Ram
39k • written 7 hours ago by
Picasa
▴ 640
1
vote
0
replies
67
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2_installation
symboliclink_error
randfold_error
9 hours ago by
Supernova
• 0
0
votes
0
replies
59
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 4 hours ago by
Ram
39k • written 9 hours ago by
Fred
• 0
2
votes
3
replies
149
views
I don't want to believe the Interproscan DB estimated download time.
time
download
Interproscan
updated 7 hours ago by
GenoMax
129k • written 14 hours ago by
gh
• 0
0
votes
1
reply
227
views
CORUM server not working?
corum
protein
complexes
database
updated 10 hours ago by
Elisabeth Gasteiger
★ 2.2k • written 11 days ago by
marta
• 0
0
votes
0
replies
55
views
Make a BedGraph file
BedGraph
RepeatMasker
BED
10 hours ago by
kirillkirilenko
▴ 10
0
votes
0
replies
68
views
Job:
PhD students in Data Science - DTU Biosustain
PhD
Data
Science
Biology
11 hours ago by
info
▴ 70
0
votes
3
replies
201
views
1000G reference panel for LD
plink
gwas
LD
13 hours ago by
en_keser
• 0
0
votes
1
reply
89
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 4 hours ago by
Ram
39k • written 13 hours ago by
chengc2016zzu
• 0
3
votes
4
replies
154
views
how to use nohup with parallel
parallel
nohup
updated 7 hours ago by
GenoMax
129k • written 15 hours ago by
gavin
• 0
0
votes
0
replies
59
views
Michigan Imputation Server - Local docker image
genotype
WGS
imputation
13 hours ago by
batch_effect
• 0
1
vote
1
reply
99
views
How do I restrict to only hm3 SNPs for plink analyses?
plink
hm3
updated 15 hours ago by
chrchang523
10k • written 19 hours ago by
garrett.ennis
• 0
0
votes
0
replies
55
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
15 hours ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
121
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
2 hours ago by
Pegasus
▴ 90
0
votes
0
replies
82
views
Merging multiple PLINK files
plink
merging
23 hours ago by
Nejla
• 0
0
votes
6
replies
1.7k
views
Using entrez-direct inside a for loop in bash
NCBI
bash
updated 23 hours ago by
GenoMax
129k • written 4.2 years ago by
Lille My
▴ 30
1
vote
1
reply
135
views
What is the best way to clean bulk RNA-seq data?
normalization
TPM
r
updated 1 day ago by
ATpoint
72k • written 1 day ago by
JACKY
▴ 80
1
vote
2
replies
208
views
how to intersect multiple bed files and get results in uncollapsed genomic intervals
bedtools
bedops
intervals
genomic
intersect
3 hours ago by
Alewa
▴ 110
0
votes
0
replies
90
views
References selected by ExomeDepth CNV
CNV
ExomeDepth
updated 23 hours ago by
GenoMax
129k • written 1 day ago by
keiko.asakura
• 0
0
votes
3
replies
374
views
ABySS genome assembler
ABySS
genome
k-mers
assembly
updated 1 day ago by
shelkmike
▴ 920 • written 3 days ago by
npavliukovec
• 0
0
votes
1
reply
139
views
Perl. How to extract CDS and gene sequence in a specified interval from GenBank files?
fasta
sequence
perl
GenBank
1 day ago by
Fungi-Beware!
• 0
0
votes
1
reply
103
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
updated 10 minutes ago by
Jesse
▴ 540 • written 1 day ago by
J.F.Jiang
▴ 900
0
votes
2
replies
163
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 1 day ago by
Ram
39k • written 1 day ago by
Joel Wallenius
▴ 120
0
votes
3
replies
651
views
Regular Expression for conversion
Linux
grep
updated 3 hours ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
1
reply
131
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 13 hours ago by
MatthewP
★ 1.2k • written 1 day ago by
barrypraveen
▴ 110
1
vote
2
replies
237
views
Retrieving allele-specific information for a variant using VEP annotation
variant-calling
VEP
COSMIC
updated 1 day ago by
Ram
39k • written 1 day ago by
bt_cepo
▴ 20
0
votes
1
reply
294
views
[Metagenome assembly] Reassembling bacterial genome using Nanopore contig/reads
illumina
nanopore
assembly
metagenome
updated 1 day ago by
Ekaterina
• 0 • written 4 weeks ago by
adhamzul
▴ 20
0
votes
2
replies
178
views
IGV grey vs white lines
minimap
nanopore
IGV
updated 1 day ago by
GenoMax
129k • written 1 day ago by
Mohd
• 0
2
votes
2
replies
155
views
featureCounts: ERROR: failed to find the gene identifier attribute
gtf
featureCounts
subread
updated 1 day ago by
GenoMax
129k • written 1 day ago by
v.berriosfarias
▴ 90
6
votes
4
replies
324
views
6 follow
Unusual FASTQ file
bioinformatics
fastqc
fastq
RNAseq
updated 1 day ago by
GenoMax
129k • written 1 day ago by
Nada
• 0
0
votes
2
replies
145
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
1 day ago by
pg45863
• 0
0
votes
1
reply
130
views
ABySS Process Killed
ABySS
genome
assembly
updated 1 day ago by
GenoMax
129k • written 1 day ago by
asarcillo
• 0
110,335 results • Page
1 of 2207
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Comment: BCR/TCR analysis using target capture sequencing data
by
Jesse
▴ 540
I still haven't tried MIXCR so I can't really answer your question itself, but, IgBLAST could give you a rough estimate of what you're look…
Comment: ERROR running Cuffmerge in reference based RNA-SEQ analysis?
by
Ram
39k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: ERROR running Cuffmerge in reference based RNA-SEQ analysis?
by
Motiar
• 0
I am also facing this problem. Did you get any solution? ``` cuffmerge -g /mnt/c/Desktop/Bioinformatic/Genome_seq/hg38.refGene.gtf -p 8 /m…
Comment: Salmon Index
by
GenoMax
129k
GENCODE is in reference to human data. GENCODE only deals with human, mouse data. You can use the Arabidopsis genome from Ensembl. Not s…
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by
Pierre Lindenbaum
154k
the formatting is missing in your question. how do you break lines ? did you add a antislash at the end of the lines ? didn't you forgot th…
Comment: Salmon Index
by
ashleymb1116
• 0
Thank you! I've made the decoy before, but I'm trying to redo it since I believe the first time I completed this incorrectly. The page Salm…
Comment: How to make a dotplot for bulk RNA average expression ?
by
LionisOne
• 0
@Trivas Thank you very much for your reply. if you don't mind could you share the script. Because its showing the dot in my plot, but I wou…
Answer: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Zhenyu Zhang
▴ 800
Where did you get the data from? which reference build and gene model is it using? There are many versions of TCGA expression data around…
Comment: gatk Hardfilter Error
by
bestone
▴ 10
A USER ERROR has occurred: Argument output was missing: Argument 'output' is required. **************************************************…
Answer: How to make a dotplot for bulk RNA average expression ?
by
Trivas
★ 1.1k
You'll want to use the `pivot_longer` function in R so that you have three columns: 1) gene, 2) condition, 3) value. You can then use ggplo…
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by
GenoMax
129k
> can I just use the cDNA file from Ensembl as mentioned above Yes you can. That said the recommendation from `salmon` devs is to use the …
Comment: Dada2 in Qiime2: losing reads during merging
by
andres.firrincieli
3.3k
How long was the amplicon? If the amplicon is longer than the sum of the two read lengths, the R1 and R2 reads will not merge. By default,…
Comment: Converting RefSeq protein accession IDs into entreZ IDs
by
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▴ 90
Thank you @genomax, since efetch function is not supported by the HPC I am working on, I replaced it with the command below; curl …
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by
LionisOne
• 0
@Pierre Lindenbaum Thanks a lot! Its a great help! I will check and let you know.
Comment: Can I send my PyMol results to a web-page as a result for a submitted query? If
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21k
Sounds like you might be better off using something like Mol*: https://academic.oup.com/nar/article/49/W1/W431/6270780?login=false https://…
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