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538 results • Page
3 of 11
Sort: Votes
Rank
Views
Votes
Replies
1
vote
3
replies
585
views
Is it wrong to use only a random subset of a dataset?
ethics
research
dataset
updated 23 days ago by
Ram
39k • written 16 months ago by
Vitor1
▴ 110
1
vote
2
replies
1.4k
views
Getting full list for DEGs in Noiseq
RNA-Seq
updated 17 days ago by
Ram
39k • written 5.4 years ago by
mubangafchama
▴ 10
1
vote
6
replies
570
views
DESeq2
heatmap
R
DESeq2
27 days ago by
Nelo
• 0
1
vote
7
replies
5.6k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 6 days ago by
dare_devil
★ 3.1k • written 5.3 years ago by
win
▴ 940
1
vote
3
replies
361
views
how to do an "reverse" oncoplot in maftools
maftools
Rstudio
updated 12 days ago by
Ram
39k • written 16 days ago by
JULIA HELENA
• 0
1
vote
3
replies
2.6k
views
Multiple Sequence Alignment Python
multiple-sequence-alignment
ClustalW
Biopython
updated 19 days ago by
Ram
39k • written 5.1 years ago by
Manu Madhavan
▴ 20
1
vote
3
replies
217
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 4 days ago by
GenoMax
129k • written 4 days ago by
mls
• 0
1
vote
2
replies
244
views
highlight regions in a dot-plot?
figure
dotplot
alignment
synteny
10 days ago by
Buffo
★ 2.2k
1
vote
5
replies
1.3k
views
WGCNA Co-expression network analysis on cuffdiff output
wgcna
cuffdiff
updated 11 days ago by
Ram
39k • written 4.7 years ago by
sbb
▴ 10
1
vote
1
reply
230
views
DownsampleSam
picard
DownsampleSam
updated 8 days ago by
Pierre Lindenbaum
154k • written 8 days ago by
mathalfilip
• 0
1
vote
0
replies
233
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 5 days ago by
Ram
39k • written 6 days ago by
Supernova
• 0
1
vote
1
reply
195
views
DESeq2 with multiple factors
DESeq2
updated 17 days ago by
jv
★ 1.2k • written 18 days ago by
Nelo
• 0
1
vote
3
replies
438
views
Need help in using dada2
dada2
R
updated 23 days ago by
Ram
39k • written 8 months ago by
rishav513
▴ 30
1
vote
1
reply
990
views
cfDNA target seq vs. cfDNA WES
cfDNA
updated 11 days ago by
Ram
39k • written 4.9 years ago by
genetic
▴ 40
1
vote
2
replies
176
views
sorting BAM file
BAM
updated 5 days ago by
ATpoint
72k • written 5 days ago by
Mohammad Amin
• 0
1
vote
14
replies
2.8k
views
How to convert Haplotypes file to PLINK format data
R
plink
updated 12 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
1
vote
3
replies
702
views
Regular Expression for conversion
Linux
grep
updated 5 days ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
1
vote
5
replies
525
views
kraken on nt library
kraken
nt
13 days ago by
Francois Piumi
▴ 30
1
vote
10
replies
2.6k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 9 days ago by
Ram
39k • written 4.2 years ago by
Kumar
▴ 100
1
vote
3
replies
1.8k
views
Translate from hsa-let- to MIMAT type
conversion
updated 23 days ago by
Ram
39k • written 6.0 years ago by
landscape95
▴ 190
1
vote
2
replies
186
views
GraphAligner/vg surject - alignment output nonsense?
vg-toolkit
graphaligner
vg
vg-surject
vgteam
26 days ago by
Andrew
▴ 20
1
vote
3
replies
330
views
Retrieve Promoter Sequences by GeneID
GeneID
by
Sequences
Retrieve
Promoter
updated 13 days ago by
lieven.sterck
14k • written 5 weeks ago by
alessandro.alma00
• 0
1
vote
3
replies
396
views
repair.sh java.lang.AssertionError
repair.sh
bbtools
updated 23 days ago by
Ram
39k • written 6 months ago by
aimanbarki
▴ 20
1
vote
1
reply
171
views
Import Pymol into Python Script
Pymol
python
updated 10 days ago by
Wayne
★ 1.8k • written 10 days ago by
jdrohan
• 0
1
vote
0
replies
116
views
mirdeep2- unable to extract files for mapping -extract_miRNAs: command not found error
miRNA
miRDeep2
miRNAanalysis
26 days ago by
Supernova
• 0
1
vote
3
replies
620
views
miRDeep2.pl error in make_html2.pl
miRNA
mirDeep
make_html2.pl
updated 20 days ago by
Ram
39k • written 20 months ago by
tikshyadav19
• 0
1
vote
0
replies
258
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics
single-cell
RNA
DEG
9 days ago by
abbas89
▴ 10
1
vote
0
replies
1.2k
views
Align two single cell experiments
R
single-cell
updated 10 days ago by
Ram
39k • written 4.5 years ago by
elb
▴ 230
1
vote
1
reply
3.1k
views
Problem with PGDSpider v 2.1.0.2
alignment
updated 4 days ago by
sackettl
▴ 20 • written 7.0 years ago by
maria.segovia.ramirez
▴ 10
1
vote
1
reply
243
views
promoter analysis
promoter
analysis
updated 29 days ago by
ATpoint
72k • written 29 days ago by
m.esmaeilpour
▴ 10
1
vote
2
replies
2.0k
views
Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
vcftools
samtools
faidx
tabix
1000Genomes
updated 13 days ago by
barslmn
★ 1.6k • written 5.6 years ago by
shrutishreyajha
▴ 10
1
vote
1
reply
239
views
Repbase not installed error while running maker
repbase
maker
updated 23 days ago by
Ram
39k • written 24 days ago by
navi_chemist
• 0
1
vote
3
replies
1.5k
views
Using SeqAn and other external libraries in C++
Read-Mapping
SeqAn
updated 18 days ago by
Ram
39k • written 5.6 years ago by
anshupa.vssut
▴ 50
1
vote
1
reply
508
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 3 days ago by
GenoMax
129k • written 3 days ago by
Mohd
▴ 20
1
vote
2
replies
211
views
Should I use mean to show variations among different studies in meta analysis
meta-analysis
R
26 days ago by
rishav513
▴ 30
1
vote
1
reply
127
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 4 days ago by
GenoMax
129k • written 4 days ago by
hashim.rana11
▴ 20
1
vote
4
replies
2.3k
views
Using a Multiple Seq Alignment tool for pairwise alignments possible?
multiple-sequence-alignment
msa
alignment
updated 19 days ago by
Ram
39k • written 7.1 years ago by
nchuang
▴ 260
1
vote
0
replies
2.5k
views
Running Multiple Alignments in MEGA with a script produces errors.
next-gen
RNA-Seq
MEGA
multiple-alignment
updated 19 days ago by
Ram
39k • written 7.2 years ago by
rachelrodgers12
▴ 10
1
vote
2
replies
232
views
Building phylogenetic tree accounting for spatial information
BEAST
IQ-TREE
COVID-19
21 days ago by
vembha
• 0
1
vote
2
replies
204
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
3 days ago by
rheab1230
▴ 140
1
vote
3
replies
1.4k
views
Alignment of two different file format
alignment
updated 19 days ago by
Ram
39k • written 5.8 years ago by
amoolya36
• 0
1
vote
1
reply
150
views
making metadata file for differential gene expression analysis
RNAseq
updated 11 days ago by
Basti
★ 1.5k • written 11 days ago by
Sara
▴ 220
1
vote
6
replies
779
views
Trimmomatic FileNotFoundException
trimmomatic
updated 23 days ago by
Ram
39k • written 10 months ago by
awhale01
• 0
1
vote
3
replies
183
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 4 days ago by
Pierre Lindenbaum
154k • written 5 days ago by
herh
• 0
1
vote
4
replies
358
views
Pre-processing for Agilent microarray data?
affymetrix
microarray
gene
agilent
rna
updated 7 days ago by
solarchan7
• 0 • written 12 days ago by
survive
• 0
1
vote
1
reply
184
views
UMI extract and deup
UMIs
24 days ago by
samuel
▴ 230
1
vote
1
reply
304
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
long
short
read
rna-seq
updated 22 days ago by
GenoMax
129k • written 23 days ago by
Jjbox
▴ 40
1
vote
3
replies
236
views
Where to upload and store annotated genetic variant data online?
mutation
annotated
cancer
database
variant
updated 20 days ago by
GenoMax
129k • written 20 days ago by
Hasib
▴ 20
1
vote
4
replies
962
views
Simulate the sequence data
next-gen-sequencing
genetics
updated 13 days ago by
Ram
39k • written 5.1 years ago by
bha
▴ 80
1
vote
2
replies
237
views
`MOFAobject@expectations` is empty list
MOFA2
updated 25 days ago by
Ram
39k • written 25 days ago by
Dan
▴ 120
538 results • Page
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Recent Replies
Answer: Installation of PPFinder
by
GenoMax
129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output
by
rpolicastro
12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl
by
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72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin
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Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
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Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
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Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG
by
jrodrigu
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Thank you so much. I made the suggested changes. However, I still have the same problem. Please check the new log file. https://github.c…
Comment: Getting same value for start and end position, "DNA methylation"
by
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72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation"
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Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output
by
bioinfo_ga
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hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by
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Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
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Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
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It works, thank you!
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Did you have any luck in splitting the BAM file based on the 10x cell barcode? I would like to split a BAM file based to only include 5 spe…
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