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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
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0
votes
0
replies
65
views
1000G reference panel for LD clumping
LD
2 days ago by
en_keser
• 0
0
votes
0
replies
78
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
3 days ago by
saladi
▴ 30
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
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
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
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
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
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
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
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
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
vote
3
replies
698
views
Regular Expression for conversion
Linux
grep
updated 3 days ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
1
reply
160
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 3 days ago by
Ram
39k • written 4 days ago by
barrypraveen
▴ 110
0
votes
2
replies
169
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
4 days ago by
pg45863
• 0
0
votes
1
reply
135
views
ABySS Process Killed
ABySS
genome
assembly
updated 4 days ago by
GenoMax
129k • written 4 days ago by
asarcillo
• 0
0
votes
0
replies
95
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
4 days ago by
narges.bioinf
• 0
0
votes
3
replies
221
views
Query qbout single cell sequencing
fastq
ScRNA
updated 3 days ago by
Ram
39k • written 4 days ago by
abbas.waseem.gcu
▴ 20
0
votes
1
reply
172
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 3 days ago by
fracarb8
▴ 950 • written 5 days ago by
Sun
• 0
0
votes
1
reply
172
views
Why coordinate sort is required in sambamba depths?
sorting
coordinate
sambamba
linux
samtools
updated 5 days ago by
Pierre Lindenbaum
154k • written 5 days ago by
MobiusT
▴ 10
0
votes
4
replies
276
views
I need help with a methyl array data analysis
methyl_array
DMPs
DMRs
beta_value
r
5 days ago by
Ahmad
▴ 10
0
votes
2
replies
242
views
Error in download library file in expression console software
expression
microarray
console
3 days ago by
Mohammad
• 0
0
votes
6
replies
335
views
Demultiplexing bam file
demultiplexing
bam_file
Iontorrent
4 days ago by
hasani.iut6
▴ 60
1
vote
2
replies
254
views
DEgs RNAseq
RNAseq
5 days ago by
Juan
• 0
0
votes
0
replies
165
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
3 days ago by
Vincent Laufer
★ 2.9k
0
votes
1
reply
238
views
problem of Global Biobank Meta-analysis Initiative
GWAS
updated 5 days ago by
Fabio Marroni
★ 3.0k • written 6 days ago by
1362321710
• 0
1
vote
1
reply
226
views
DownsampleSam
picard
DownsampleSam
updated 6 days ago by
Pierre Lindenbaum
154k • written 6 days ago by
mathalfilip
• 0
0
votes
1
reply
230
views
Error while running Megahit
Megahit
updated 5 days ago by
Mensur Dlakic
★ 23k • written 6 days ago by
abhiramiabhirami9072
• 0
2
votes
5
replies
403
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
3 days ago by
DanielEB_fisk
• 0
0
votes
0
replies
193
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
7 days ago by
dima
• 0
1
vote
0
replies
251
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics
single-cell
RNA
DEG
7 days ago by
abbas89
▴ 10
0
votes
1
reply
753
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure
pymol
protein
pdb
python
updated 3 days ago by
Joe
21k • written 7 days ago by
Aatif Hashmi
• 0
0
votes
1
reply
299
views
Deferentially expressed gene with high log2foldchange by DESeq2; but not meaningful at the individual level
DESeq2
RNA-seq
DGEA
updated 7 days ago by
Vincent Laufer
★ 2.9k • written 7 days ago by
Sara
▴ 10
1
vote
2
replies
264
views
Abyss taking a Long time to run
abyss
assembly
genome
fastq
7 days ago by
Maliha
▴ 20
0
votes
2
replies
280
views
Import or read Snapgene .dna files into R
R
.dna
snapgene
7 days ago by
eggrandio
▴ 40
4
votes
4
replies
343
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 3 days ago by
Joe
21k • written 7 days ago by
antoine.fauchois92
▴ 20
0
votes
0
replies
157
views
BEAST Divergence time Analysis
time
BEAST
BEAUti
divergence
7 days ago by
ahmadjoyyia
▴ 10
0
votes
0
replies
173
views
Differential Gene Expression analysis in heterogeneous tissues
RNA-seq
deseq2
updated 7 days ago by
Ram
39k • written 7 days ago by
txema.heredia
▴ 70
1
vote
1
reply
228
views
Variant Annotation
Variant-Annotation
VCF
R
updated 7 days ago by
Ram
39k • written 7 days ago by
Chethana
• 0
0
votes
1
reply
250
views
too many zeros in 16S rRNA amplicon sequencing data
16S
rRNA
updated 6 days ago by
andres.firrincieli
3.3k • written 7 days ago by
zhangdengwei
▴ 180
0
votes
1
reply
206
views
Finding Kinetic Parameters from Western Blot images
image-processing
western-blot
updated 7 days ago by
Ram
39k • written 7 days ago by
Vijeth
• 0
0
votes
0
replies
161
views
Chipseq data peak calling issue
ChIP-seq
RNA
sequencing
updated 3 days ago by
Ram
39k • written 7 days ago by
Adyasha
• 0
1,000 results • Page
2 of 20
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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154k
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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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