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499 results • Page
1 of 10
Sort: Views
Rank
Views
Votes
Replies
115
votes
52
replies
85k
views
21 follow
How to plot coverage and depth statistics of a bam file
bam
coverage
depth
next-gen-sequencing
updated 4 days ago by
Ram
37k • written 8.6 years ago by
kay
▴ 320
166
votes
41
replies
83k
views
27 follow
Multiline Fasta To Single Line Fasta
sequence
fasta
updated 5 days ago by
Onur
• 0 • written 11.6 years ago by
Palu
▴ 240
9
votes
7
replies
42k
views
R programming: compare columns to column and get the mismatch
R
updated 3 days ago by
Ram
37k • written 7.8 years ago by
MAPK
★ 2.0k
27
votes
15
replies
40k
views
16 follow
how to unzip the files in batch?
next-gen
RNA-Seq
SNP
alignment
updated 3 days ago by
Ram
37k • written 7.7 years ago by
flavobacteria
▴ 50
205
votes
58
replies
38k
views
31 follow
Forum:
Will Python Take The Place Of R?
biopython
statistics
r
python
Forum
updated 5 days ago by
Ram
37k • written 9.7 years ago by
Medhat
9.5k
28
votes
14
replies
37k
views
8 follow
Running and Analyzing fastqc on multiple fastq files
next-gen
RNA-Seq
genome
updated 1 day ago by
Ram
37k • written 7.7 years ago by
ravi.uhdnis
▴ 220
92
votes
105
replies
32k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial
1000
genomes
PCA
PLINK
updated 4 days ago by
s.w.vanderlaan
▴ 40 • written 4.4 years ago by
Kevin Blighe
84k
40
votes
10
replies
32k
views
7 follow
Can'T Locate Vcf.Pm Vcftools
vcftools
vcf
updated 1 day ago by
Ram
37k • written 11.2 years ago by
Deniz
▴ 210
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
fastq
trimming
qc
tutorial
Tutorial
updated 5 days ago by
Ram
37k • written 10.4 years ago by
Istvan Albert
96k
117
votes
59
replies
29k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware
next-gen
updated 1 day ago by
Ram
37k • written 7.7 years ago by
Angelo Victoria
▴ 30
25
votes
35
replies
28k
views
16 follow
Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
mpileup
updated 4 days ago by
Jan Röslein
▴ 10 • written 8.9 years ago by
komal.rathi
★ 4.0k
296
votes
121
replies
24k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 4 days ago by
jena
▴ 240 • written 12.6 years ago by
Eric Normandeau
11k
13
votes
8
replies
24k
views
How to generate a fasta file from a python dictionary or lists?
sequence
fasta
list
dictionary
python
updated 4 days ago by
Ram
37k • written 7.7 years ago by
grayapply2009
▴ 240
38
votes
11
replies
20k
views
11 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq
DESeq2
geneontology
GSEA
updated 4 days ago by
Oliver
• 0 • written 5.3 years ago by
Sreeraj Thamban
▴ 280
87
votes
16
replies
19k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat
batch-effect
sva
updated 6 days ago by
madbadradscientist
▴ 20 • written 7.7 years ago by
Christian
★ 3.0k
11
votes
8
replies
19k
views
7 follow
Convert Ensembl Transcript Ids Ensmust To Gene Symbol Using Mygene Module In Python
python
ensembl
convert
gene
updated 5 days ago by
Francesco
• 0 • written 9.0 years ago by
hicsuntdrac0nis
▴ 240
27
votes
50
replies
15k
views
7 follow
Extract fasta sequences from a large file using a list of names
16s
fasta
extract
updated 1 day ago by
Ram
37k • written 7.8 years ago by
fhsantanna
▴ 600
4
votes
8
replies
14k
views
[WGCNA] Error in goodSamplesGenes function
RNA-Seq
wgcna
R
updated 3 days ago by
Ram
37k • written 8.0 years ago by
gustavoborin01
▴ 90
59
votes
95
replies
14k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA
CNV
genes
updated 1 day ago by
Di
▴ 10 • written 4.8 years ago by
Chaimaa
▴ 260
2
votes
3
replies
13k
views
Bootstrap values on a phylogenetic tree (RAxML).
PAxML
bootstrap
phylogenetic-tree
updated 2 days ago by
Ram
37k • written 7.7 years ago by
vasilislenis
▴ 150
10
votes
8
replies
13k
views
6 follow
Is the heterozygosity flag (--het) in vcftools calculate observed and expected heterozygosity?
vcftools
vcf
updated 1 day ago by
dr.fakharunnisa
• 0 • written 5.5 years ago by
ahmedaljumiliy
▴ 40
9
votes
11
replies
12k
views
6 follow
Extracting Reads Containing A Specific Variant From A Bam File
bam
sam
format
cigar
updated 6 days ago by
craigdj91
• 0 • written 9.2 years ago by
Nick Stoler
▴ 70
11
votes
10
replies
11k
views
Can Limma package be used for RNA-Seq Differential gene expression analysis for Quantile normalized log transformed RPKM data
RNA-Seq
limma
TCGA
updated 1 day ago by
Ram
37k • written 7.7 years ago by
David_emir
▴ 460
9
votes
3
replies
9.3k
views
How to correctly use the color option in R image() function?
R
image
updated 2 days ago by
Ram
37k • written 7.7 years ago by
Xianjun
▴ 300
23
votes
17
replies
9.2k
views
7 follow
deinterleave fastq file
fastq
bamtofastq
updated 1 day ago by
Ram
37k • written 7.8 years ago by
anon
▴ 50
5
votes
3
replies
9.0k
views
STRUCTURE software for GBS SNP data
software-error
SNP
updated 1 day ago by
Ram
37k • written 7.9 years ago by
dinesh
▴ 50
14
votes
9
replies
8.1k
views
7 follow
Hg19 Coordinate To Cds Position
mapping
genomics
coordinates
cds
position
updated 4 days ago by
Ram
37k • written 10.8 years ago by
Halit
▴ 90
8
votes
6
replies
8.1k
views
6 follow
Quadruplex sequence batch prediction
Quadruplex
updated 1 day ago by
Ram
37k • written 7.7 years ago by
Qi Zhao
▴ 50
9
votes
12
replies
8.0k
views
Ensembl GTF format: isn't the tag "transcript_id" mandatory?
annotation
RNA-Seq
GTF
GFF
ensembl
updated 2 days ago by
Ram
37k • written 7.8 years ago by
Pfs
▴ 550
17
votes
23
replies
7.9k
views
13 follow
How To Assemble Chloroplast Genome?
genome
assembly
updated 4 days ago by
Ram
37k • written 10.8 years ago by
Biomonika (Noolean)
3.2k
5
votes
7
replies
7.5k
views
[solved] Retrieve fasta from balst db using blastdbcmd: Error: gi|742519789: OID not found
software error
blast
updated 1 day ago by
Ram
37k • written 7.7 years ago by
dago
★ 2.7k
13
votes
4
replies
7.4k
views
Selection of a "suggestive" level of association in a GWAS study
association
statistics
GWAS
updated 1 day ago by
Ram
37k • written 7.7 years ago by
Vincent Laufer
★ 2.5k
1
vote
10
replies
7.3k
views
How to change fastq reads header for running Trinity on them?
trinity
RNA-Seq
ngs
Assembly
updated 13 hours ago by
Ram
37k • written 7.7 years ago by
seta
★ 1.7k
8
votes
8
replies
7.3k
views
ANI calculation: alternatives to Jspecies
ani
jspecies
updated 3 days ago by
Ram
37k • written 7.7 years ago by
fhsantanna
▴ 600
8
votes
15
replies
7.1k
views
How to perform multiple comparisons using edgeR?
RNA-Seq
edgeR
updated 1 day ago by
ryandward
• 0 • written 3.7 years ago by
silas008
▴ 150
0
votes
3
replies
6.7k
views
RNA-seq experiment validation by qPCR
RNA-Seq
updated 1 day ago by
Ram
37k • written 7.7 years ago by
Inbalor
▴ 20
3
votes
11
replies
6.7k
views
6 follow
Extract vcf file header and save it in Key-Value csv
genome
SNP
next-gen-sequencing
updated 4 days ago by
Ram
37k • written 4.2 years ago by
tinyskinn
• 0
5
votes
5
replies
6.7k
views
filtering by POS in bcftools
software error
bcftools
updated 4 days ago by
jediknightchannel
• 0 • written 4.0 years ago by
4galaxy77
2.6k
2
votes
3
replies
6.6k
views
Multiple sequence alignment of sequenecs of different length
multiple-sequence-alignment
updated 1 day ago by
Ram
37k • written 7.7 years ago by
rosies
• 0
2
votes
7
replies
6.6k
views
Bowtie2 run out of memory
software-error
alignment
bowtie2
updated 1 day ago by
Ram
37k • written 7.7 years ago by
anon
▴ 50
10
votes
7
replies
6.3k
views
How much paired end vs single end RNA-seq reads can have influnce on expression level quantification ?
alignment
RNA-Seq
next-gen-sequencing
updated 2 days ago by
Ram
37k • written 7.7 years ago by
jack
▴ 960
21
votes
10
replies
6.1k
views
6 follow
Randomize Read Order In Multigbp Fastq File?
fastq
updated 3 days ago by
sovrappensiero
▴ 50 • written 11.6 years ago by
2184687-1231-83-
★ 5.0k
2
votes
3
replies
5.6k
views
How to get the abundance of genes in metagenomes from MG RAST
abundance
mg-rast
metagenome
updated 1 day ago by
Ram
37k • written 8.3 years ago by
khorms
▴ 220
3
votes
13
replies
5.5k
views
Error in Package GEOquery
Microarray-data
bioconductor
GEOquery
R
updated 1 day ago by
Ram
37k • written 7.7 years ago by
pankajnarula84
▴ 10
4
votes
3
replies
5.5k
views
Convert Official Gene Symbols To Uniprot Ids In Python ?
convert
gene
uniprot
python
database
updated 5 days ago by
Francesco
• 0 • written 9.0 years ago by
hicsuntdrac0nis
▴ 240
28
votes
21
replies
5.5k
views
7 follow
Bash tutorial for biologists?
bash
updated 1 day ago by
Ram
37k • written 7.7 years ago by
Parham
★ 1.6k
1
vote
5
replies
5.5k
views
Statistical tests for RPKM comparison
RPKM
differential-gene-expression
updated 1 day ago by
Ram
37k • written 7.7 years ago by
rpjl1230
▴ 20
1
vote
6
replies
5.4k
views
How to Normalize the Microarray Data Obtained from ncbi?
microarray
normalization
ncbi
Bioconductor
R
updated 1 day ago by
Ram
37k • written 7.7 years ago by
pankajnarula84
▴ 10
19
votes
16
replies
5.1k
views
10 follow
Is Smith Waterman ever used?
alignment
sequence
updated 3 days ago by
Ram
37k • written 7.7 years ago by
mikko732
▴ 60
0
votes
3
replies
5.0k
views
QQ plot - how to add gris shadow showing confidence interval
qqplot
R
updated 5 days ago by
Ram
37k • written 7.7 years ago by
aleix.arnau1990
▴ 10
499 results • Page
1 of 10
Recent Votes
Deseq2 with one factor and multiple levels
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SNP calling
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1000 genomes project reference panel - GRCh38
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Recent Replies
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
If you aren't willing to provide more precise information than this, sufficient for a reader to reproduce what you're seeing, I will delete…
Answer: Error while trying to install salmon
by
Chris
▴ 10
Donwloading the package from conda (https://anaconda.org/conda-forge/boost/files?version=1.60.0) worked for me wget https://anaconda.org/…
Answer: finding error to run edgeR, error in ploting MDS and after that in model matrix
by
Gordon Smyth
★ 5.4k
First issue is that GEO series matrix files can't be read using `read.delim`. Second issue is the data are from Agilent microarrays and …
Comment: PLINK2 selecting variants based on INFO score
by
m.c.roozen
• 0
I have tried that (the .pvar file contains the "1:10586" form as ID which I mentioned above) which leads to the same output as above, 0 var…
Answer: samtools markdup in Rsamtools
by
joe
▴ 350
You can run any system command from inside R using `system()`. This works well if there is a single command without many dependencies. For …
Comment: samtools markdup in Rsamtools
by
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152k
> But other solutions are also fine: bash, nextflow, snakemake
Answer: samtools markdup in Rsamtools
by
ATpoint
68k
My honest opinion: Do processing of sequencing data on the standard command line with samtools. There is no need for the added complexity t…
Comment: To batch correct or analyse separately?
by
predeus
★ 1.8k
Another great and up-to-date resource is this: https://www.sc-best-practices.org/preamble.html
Comment: PLINK2 selecting variants based on INFO score
by
chrchang523
9.9k
The --exclude file must use the same variant IDs as your .pvar file. You should elaborate on what seemed to go wrong when you tried to arr…
Comment: phylogeny
by
炫
• 0
Hello, my problem is the same as yours, did you finally solve this problem?
Comment: phylogeny
by
炫
• 0
您好,我的问题和您的一模一样,请问您这个问题最终解决了吗
Comment: Issue with hmmcalibrate during tutorial.
by
apcreyes29
• 0
If that's the case then I'll just proceed then. Thank you!
Answer: To batch correct or analyse separately?
by
ATpoint
68k
Instead of writing that all down I recommend to read the relevant part of the Bioconductor scRNA-seq book (OSCA) which covers the "how's" a…
Answer: Issue with hmmcalibrate during tutorial.
by
Mensur Dlakic
★ 22k
Pretty sure that `hmmcalibrate` does not exist in HMMer version 3+ as the models are internally calibrated. I think you are using a manual …
Comment: High downstream gene expression
by
yoser4
▴ 10
Thank you for your reply. Your answer has helped me. I am a novice in scientific research, and the reading of literature is really poor. …
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