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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
23
votes
22
replies
49k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 17 months ago by
Nicole
• 0 • written 6.0 years ago by
gaelgarcia
▴ 260
4
votes
4
replies
41k
views
How to convert a URL into a DOI programmatically
pubmed
doi
url
written 7.6 years ago by
entheologist33
▴ 100
4
votes
13
replies
35k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 22 months ago by
Qboy
▴ 10 • written 6.1 years ago by
sambioinfo2018
▴ 20
20
votes
15
replies
30k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 21 months ago by
Ram
43k • written 8.3 years ago by
dam4l
▴ 200
5
votes
6
replies
29k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools
linux
data
5.0 years ago by
star
▴ 350
2
votes
3
replies
28k
views
How to extract vcf.gz and vcf.gz.tbi
SNP
sequence
gene
updated 5.8 years ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
elhlalisoufiane
▴ 30
3
votes
4
replies
23k
views
Using nr database for BLAST search
nr
database
blast
blastp
updated 7.6 years ago by
Biostar
20 • written 7.8 years ago by
cookm346
▴ 20
13
votes
4
replies
23k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage
depth
read depth
7.0 years ago by
ariel.balter
▴ 260
28
votes
17
replies
22k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
2.4 years ago by
Leite
★ 1.3k
3
votes
3
replies
21k
views
Subsetting - Raw Counts from Seurat Object
seurat
raw counts
RNA-Seq
4.0 years ago by
David_emir
▴ 490
2
votes
4
replies
21k
views
Error in file(file, "rt") : cannot open the connection
R
MicroRNA TXT FORMAT
updated 8.0 years ago by
GenoMax
141k • written 8.0 years ago by
31sharmajittu1991
• 0
7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
7.7 years ago by
aggregatibacter
▴ 180
1
vote
5
replies
19k
views
Calculating the sequence similarity and percentage of matched sequences
alignment
sequence
updated 6.4 years ago by
eteleeb
• 0 • written 6.5 years ago by
ago1mutant
▴ 10
2
votes
8
replies
18k
views
Using vcfutils.pl command
alignment
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
lcc1844
▴ 40
2
votes
10
replies
18k
views
How do you use the Aspera ascp command?
aspera
gigascience
gigaDb
updated 2.6 years ago by
Ram
43k • written 8.5 years ago by
cyril-cros
▴ 950
13
votes
13
replies
17k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
4.7 years ago by
Arindam Ghosh
▴ 510
16
votes
38
replies
17k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
16
votes
14
replies
17k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.8 years ago by
salamandra
▴ 550
2
votes
13
replies
17k
views
convert text file to fasta file
blast
updated 7.7 years ago by
GouthamAtla
12k • written 7.7 years ago by
sukesh1411
▴ 30
4
votes
18
replies
17k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.5 years ago by
Biostar
20 • written 5.7 years ago by
Shelle
▴ 30
1
vote
8
replies
17k
views
How to update rlang in R?
rlang
R
18 months ago by
Amr
▴ 160
1
vote
5
replies
16k
views
pheatmap: how to use legend information as row annotation?
R
pheatmap
legend
annotation
6.0 years ago by
n85825
• 0
5
votes
4
replies
16k
views
glmnet package lasso error
glmnet
lasso
multilinear regression
6.1 years ago by
demoraesdiogo2017
▴ 100
0
votes
3
replies
16k
views
How to choose a TPM cut-off point
RNA-Seq
transcript
tpm
updated 20 months ago by
Ram
43k • written 8.5 years ago by
amyfm
▴ 10
6
votes
2
replies
16k
views
Pacbio Ccs Vs Subreads Explained ?
updated 10.0 years ago by
Biostar
20 • written 10.5 years ago by
curious.genome
▴ 40
0
votes
8
replies
16k
views
find ORF in sequence python
sequence
updated 7.3 years ago by
natasha.sernova
★ 4.0k • written 7.3 years ago by
elisheva
▴ 120
3
votes
8
replies
16k
views
Error when running pheatmap
pheatmap
Error in hclust
5.1 years ago by
luzglongoria
▴ 50
2
votes
4
replies
16k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 18 months ago by
Ram
43k • written 8.7 years ago by
meekadi
▴ 10
4
votes
10
replies
16k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 6.0 years ago by
GenoMax
141k • written 6.0 years ago by
WUSCHEL
▴ 750
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE
insert-size
7.8 years ago by
Ric
▴ 430
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 10 months ago by
Ram
43k • written 5.6 years ago by
Shahzad
▴ 30
8
votes
4
replies
15k
views
Use of if-else statement in snakemake rule
snakemake
if-else
python
updated 4.4 years ago by
schroder.julia
• 0 • written 6.8 years ago by
Jokhe
▴ 140
0
votes
3
replies
15k
views
How to change/remove name of annotation ComplexHeatmap package?
ComplexHeatmap
R
RNA-Seq
annotations
updated 3.9 years ago by
Ram
43k • written 3.9 years ago by
camillab.
▴ 160
1
vote
8
replies
15k
views
HTSeq-count high number of no_feature
htseq-count
rna-seq
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
cafelumiere12
▴ 80
4
votes
1
reply
15k
views
Converting BigBed to Bed format
Installing BigFile Support
8.9 years ago by
sumaira.zaman10
▴ 20
6
votes
13
replies
15k
views
Fastq file is truncated error message
RNA-Seq
error
fastq
7.9 years ago by
rob.costa1234
▴ 310
4
votes
1
reply
15k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq
TPM
STAR
salmon
quantification
7.3 years ago by
ZheFrench
▴ 570
1
vote
13
replies
15k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 2.9 years ago by
darklings
▴ 570 • written 4.5 years ago by
gordo2b
• 0
9
votes
13
replies
15k
views
GC Content of Fasta file --- Python Help
sequence
7.2 years ago by
Patrick Brennan
▴ 50
0
votes
3
replies
14k
views
Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character
inSilicoMerging
9.9 years ago by
ira_grich
• 0
0
votes
2
replies
14k
views
Error in -delete: invalid argument to unary operator
RNA-Seq
R
4.2 years ago by
ovariohisterectomia
▴ 40
6
votes
13
replies
14k
views
Showing FDR and log2FC in Volcano plot using R
R
RNA-Seq
volcano plot
updated 4.9 years ago by
zx8754
11k • written 6.4 years ago by
Farbod
★ 3.4k
8
votes
5
replies
14k
views
The comparison between HISAT2 and Tophat2
RNA-Seq
Tophat2
HISAT2
updated 5.6 years ago by
Ram
43k • written 8.2 years ago by
Peng Huang
▴ 50
0
votes
2
replies
13k
views
How to download pfam database
sequence
updated 7.3 years ago by
Medhat
9.7k • written 7.3 years ago by
Sanchita Gupta
▴ 30
4
votes
12
replies
13k
views
STAR alignment error- Segmentation fault (core dumped)
alignment
software error
RNA-Seq
STAR
5.8 years ago by
EagleEye
7.5k
2
votes
1
reply
13k
views
Rename Idents in Seurat Object
RNA-Seq
3.9 years ago by
Thorerges
▴ 10
3
votes
11
replies
13k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq
RNA-Seq
STAR
updated 2.0 years ago by
Ram
43k • written 9.3 years ago by
noushin.farnoud
▴ 130
0
votes
2
replies
13k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq
GSEA
gene
genome
updated 4.7 years ago by
Morris_Chair
▴ 350 • written 4.7 years ago by
limjustinj
• 0
0
votes
4
replies
13k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 18 months ago by
Ram
43k • written 8.7 years ago by
Debbie
▴ 10
1
vote
2
replies
13k
views
kart file in prefetch
rna-seq
updated 7.5 years ago by
Biostar
20 • written 7.6 years ago by
zh.khodadadi
▴ 20
1,000 results • Page
1 of 20
Recent Votes
Comment: Adding CB tag to bam file
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
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Recent Replies
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
b.contreras.moreira
▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM
by
VITALA
• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result
by
ahmad.sajad4541
• 0
Thank you so much. Should i proceed for annotation step?
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
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