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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
149
views
Which type of variant caller should I use in a WES normal cell line sample?
variant-caller
WES
updated 2 days ago by
ATpoint
72k • written 2 days ago by
bompipi95
▴ 120
5
votes
4
replies
173
views
Alignment of case vs. control from different origin
Alignment
RNAseq
updated 2 days ago by
i.sudbery
17k • written 2 days ago by
sativus
• 0
0
votes
2
replies
231
views
Peaks annotation on bacterial genome
ChIPpeakAnno
annotation
bacteria
2 days ago by
Maurice
• 0
1
vote
1
reply
102
views
Create customized gene annotation file
reference-genome
cellranger
updated 2 days ago by
Ram
39k • written 2 days ago by
rhonddaskl
• 0
0
votes
0
replies
71
views
metagenomics data - AMR genes
amr
resistome
resistance
ARG
metagenomics
2 days ago by
aziznasr1920
▴ 10
1
vote
3
replies
163
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 1 day ago by
Pierre Lindenbaum
154k • written 2 days ago by
herh
• 0
0
votes
0
replies
65
views
1000G reference panel for LD clumping
LD
2 days ago by
en_keser
• 0
6
votes
25
replies
29k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 2 days ago by
13554221497
• 0 • written 5.2 years ago by
ARich
▴ 130
160
votes
63
replies
76k
views
38 follow
Selecting Random Pairs From Fastq?
random
fastq
illumina
sequence
updated 2 days ago by
Ram
39k • written 12.2 years ago by
Ketil
4.1k
4
votes
5
replies
13k
views
Take A Subset Of A Fastq Paired-End Sample
paired-end
fastq
rna-seq
illumina
updated 2 days ago by
Ram
39k • written 10.2 years ago by
dfernan
▴ 730
2
votes
2
replies
169
views
Forum:
Colleges
Colleges
india
universities
updated 2 days ago by
Ram
39k • written 2 days ago by
mahimanepalli36
• 0
3
votes
5
replies
235
views
Concatenating text files based on common indices
Bash
Python
updated 2 days ago by
Ram
39k • written 2 days ago by
Hau Tak Leighton
• 0
1
vote
8
replies
383
views
how to create correlation matrix R
pearson-correlation
R
1 day ago by
satva72
• 0
0
votes
0
replies
78
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
3 days ago by
saladi
▴ 30
8
votes
5
replies
336
views
I don't want to believe the Interproscan DB estimated download time.
Interproscan
2 days ago by
gh
• 0
1
vote
7
replies
282
views
RNAseq Data and Pipeline
RNA-Seq
DESeq2
Differential-Gene-Expression
updated 3 days ago by
Ram
39k • written 3 days ago by
turcoa1
• 0
0
votes
2
replies
600
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 3 days ago by
Ram
39k • written 12 months ago by
Meeran
• 0
0
votes
7
replies
549
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 2 days ago by
Vincent Laufer
★ 2.9k • written 6 days ago by
Camilo Andres
▴ 30
0
votes
3
replies
181
views
How to make a dotplot for bulk RNA average expression ?
Dotplot
RNA-seq
updated 3 days ago by
bhumm
▴ 40 • written 3 days ago by
LionisOne
• 0
0
votes
3
replies
187
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 2 days ago by
andres.firrincieli
3.3k • written 3 days ago by
kamanovae
▴ 80
0
votes
1
reply
147
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 3 days ago by
GenoMax
129k • written 3 days ago by
fafad046
• 0
3
votes
6
replies
276
views
Salmon Index
transcriptomics
Bulk
RNA-sequencing
updated 3 days ago by
GenoMax
129k • written 3 days ago by
ashleymb1116
• 0
1
vote
4
replies
559
views
Expected number of haplotype IDs per path in PHG
PHG
updated 3 days ago by
Ram
39k • written 6 weeks ago by
twrl8
• 0
0
votes
3
replies
175
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
1 day ago by
Mohd
▴ 20
1
vote
2
replies
158
views
sorting BAM file
BAM
updated 2 days ago by
ATpoint
72k • written 3 days ago by
Mohammad Amin
• 0
0
votes
1
reply
99
views
Search SRA metadata for Histological_Type and Body_Site
sra
updated 3 days ago by
GenoMax
129k • written 3 days ago by
oakhamwolf
▴ 20
2
votes
3
replies
218
views
NCBI refseq ids to uniprot ids
refseq
Uniprot
updated 3 days ago by
Ram
39k • written 3 days ago by
t.ali
• 0
3
votes
3
replies
159
views
Covert multiple short sequence into list of IUPAC motif
sequence
updated 3 days ago by
GenoMax
129k • written 3 days ago by
praasu
▴ 40
1
vote
0
replies
88
views
Resequencing data of pangenome
NGS
PanGenome
Resequence
updated 3 days ago by
Ram
39k • written 3 days ago by
bioinfo223
▴ 10
4
votes
2
replies
190
views
Graphing Average Expression of Group of Genes
Boxplot
R
updated 3 days ago by
Shred
★ 1.2k • written 3 days ago by
cthangav
▴ 40
0
votes
0
replies
82
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 3 days ago by
zx8754
11k • written 3 days ago by
sidrah.maryam
▴ 50
0
votes
1
reply
143
views
Seurat: How to get all genes name of a cell ?
seurat
updated 3 days ago by
jv
★ 1.2k • written 3 days ago by
Picasa
▴ 640
1
vote
0
replies
223
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 3 days ago by
Ram
39k • written 3 days ago by
Supernova
• 0
0
votes
0
replies
100
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 3 days ago by
Ram
39k • written 3 days ago by
Fred
• 0
0
votes
1
reply
269
views
CORUM server not working?
corum
protein
complexes
database
updated 3 days ago by
Elisabeth Gasteiger
★ 2.2k • written 14 days ago by
marta
• 0
0
votes
0
replies
130
views
Job:
PhD students in Data Science - DTU Biosustain
PhD
Biology
Data-Science
updated 3 days ago by
Ram
39k • written 3 days ago by
info
▴ 70
0
votes
3
replies
248
views
1000G reference panel for LD
plink
gwas
LD
3 days ago by
en_keser
• 0
0
votes
1
reply
142
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 3 days ago by
Ram
39k • written 3 days ago by
chengc2016zzu
• 0
3
votes
4
replies
207
views
how to use nohup with parallel
parallel
nohup
updated 3 days ago by
GenoMax
129k • written 3 days ago by
gavin
• 0
1
vote
1
reply
134
views
How do I restrict to only hm3 SNPs for plink analyses?
plink
hm3
updated 3 days ago by
chrchang523
10k • written 4 days ago by
garrett.ennis
• 0
0
votes
0
replies
81
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
3 days ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
195
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
2 days ago by
Pegasus
▴ 90
0
votes
0
replies
114
views
Merging multiple PLINK files
plink
merging
4 days ago by
Nejla
• 0
0
votes
6
replies
1.7k
views
Using entrez-direct inside a for loop in bash
NCBI
bash
updated 4 days ago by
GenoMax
129k • written 4.2 years ago by
Lille My
▴ 30
1
vote
2
replies
266
views
how to intersect multiple bed files and get results in uncollapsed genomic intervals
bedtools
bedops
intervals
genomic
intersect
3 days ago by
Alewa
▴ 110
0
votes
0
replies
114
views
References selected by ExomeDepth CNV
CNV
ExomeDepth
updated 4 days ago by
GenoMax
129k • written 4 days ago by
keiko.asakura
• 0
0
votes
3
replies
419
views
ABySS genome assembler
ABySS
genome
k-mers
assembly
updated 4 days ago by
shelkmike
▴ 920 • written 6 days ago by
npavliukovec
• 0
1
vote
1
reply
203
views
Perl. How to extract gene entry, CDS and gene sequence from a specified range from GenBank files?
fasta
sequence
GenBank
perl
2 days ago by
Fungi-Beware!
▴ 10
0
votes
2
replies
215
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
2 days ago by
J.F.Jiang
▴ 900
0
votes
2
replies
195
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 4 days ago by
Ram
39k • written 4 days ago by
Joel Wallenius
▴ 130
1,000 results • Page
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Recent Votes
Efficiently extract alignments with NH:i:1 field
Help with Samtools flags to get only primary, unique, non duplicate aligned reads
Answer: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
Comment: Optimum setting for local blastp for ~10K sequences
Perl. How to extract gene entry, CDS and gene sequence from a specified range from GenBank files?
Comment: How to sort gff3 according to chromosome order?
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Comment: Help with running ATAC using Encode pipeline
by
Chris
▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs
by
rycro_c
• 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage
by
Dave Carlson
★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order?
by
Pierre Lindenbaum
154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage
by
GenoMax
129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences
by
GenoMax
129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files
by
Joe
21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
GenoMax
129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order?
by
GenoMax
129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column
by
atemedorri137798
• 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order?
by
Ram
39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
Comment: How to sort gff3 according to chromosome order?
by
BioinfoBee
• 0
using sort -k1,1 doesn't keep the order of child features of each gene in output.
Comment: How to sort gff3 according to chromosome order?
by
Ram
39k
You're sorting by chromosome AND co-ordinates. Try just `sort -k1,1`
Comment: How to sort gff3 according to chromosome order?
by
BioinfoBee
• 0
it does sort but not able to keep the child features (mRNA, CDS, exon) in proper order. For example, I can sort using: sort -k1,1 -k4,4n -k…
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