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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
14
votes
18
replies
4.9k
views
GATK Haplotype Caller
next-gen
GATK
haplotype
caller
contigs
updated 7.3 years ago by
Biostar
20 • written 7.5 years ago by
plink_9857
▴ 50
16
votes
18
replies
5.5k
views
8 follow
Python Program to read .fasta file to .txt file
Python
updated 4.7 years ago by
Mensur Dlakic
★ 27k • written 4.7 years ago by
tikshyadav19
• 0
3
votes
18
replies
1.9k
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
18 months ago by
lacb
▴ 120
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
22 days ago by
b.contreras.moreira
▴ 170
0
votes
18
replies
1.9k
views
freebayes error variant calling
snp
3.7 years ago by
evelyn
▴ 230
4
votes
18
replies
3.0k
views
Inline barcodes in the reverse reads
barcodes
7.5 years ago by
Picasa
▴ 640
5
votes
18
replies
6.7k
views
EnhancedVolcano plot error: Log2foldchange is not numeric!
R
EnhancedVolcano
4.4 years ago by
michelle.piquet
▴ 60
1
vote
18
replies
2.7k
views
Why big gaps when I use Entrez Eutils to download protein coding sequences.
entrez
eutils
7.7 years ago by
Tom
▴ 40
0
votes
18
replies
1.8k
views
bcl2fastq conversion with specifying exact match of indices
genome
RNA-Seq
sequencing
updated 8 months ago by
GenoMax
141k • written 8 months ago by
Apex92
▴ 280
20
votes
17
replies
6.0k
views
HiSeq 4000 PhiX screening and removal using bbduk
spikein
filtering
bbmap
bbduk
phix
6.7 years ago by
Anand Rao
▴ 630
7
votes
17
replies
4.3k
views
Strange MA-plot using DESeq2
rna-seq
R
deseq2
updated 7.3 years ago by
Biostar
20 • written 7.4 years ago by
stan
▴ 80
5
votes
17
replies
4.3k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics
encode
10.1 years ago by
14134125465346445
★ 3.6k
5
votes
17
replies
8.5k
views
Removing fastq duplicates
sequence
next-gen
ChIP-Seq
3.4 years ago by
C4
▴ 30
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
12
votes
17
replies
4.9k
views
How do I generate all possible Newick Tree permutations for a set of species given an outgroup in Python?
Python
Newick
phylogenetics
tree
phylogeny
6.5 years ago by
anonymous1192976466
▴ 50
7
votes
17
replies
3.9k
views
How to find the differences in aligned bam files
RNA-Seq
7.2 years ago by
1769mkc
★ 1.2k
4
votes
17
replies
2.8k
views
Any strategy to find out the reason of having unusual Coefficient of Variation (CV) for gene expression data?
microarray
gene-expression
CV
error
4.8 years ago by
Jurat Shahidin
▴ 100
0
votes
17
replies
4.9k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 19 months ago by
Ram
43k • written 8.6 years ago by
jigarnt
▴ 30
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.5 years ago by
dimitrischat
▴ 210
2
votes
17
replies
2.9k
views
Snakemake Megahit error
megahit
Snakemake
2.4 years ago by
blackadder
▴ 30
6
votes
17
replies
2.4k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen
assembly
genome
alignment
5.8 years ago by
williamsbrian5064
▴ 510
0
votes
17
replies
3.6k
views
WGCNA error: "Error in cutreeDynamic"
rna-seq
wgcna
software error
R
next-gen
updated 2.3 years ago by
Dio
• 0 • written 5.6 years ago by
giuseppe0525
▴ 20
1
vote
17
replies
4.2k
views
Error executing bedops convert2bed
bedops
bed
vcf
convert2bed
7.3 years ago by
lakhujanivijay
5.8k
20
votes
17
replies
3.2k
views
How to add "transcript" feature to a gtf file?
gtf
updated 9 months ago by
1769mkc
★ 1.2k • written 3.2 years ago by
pomodoro_sinensis
▴ 110
9
votes
17
replies
2.2k
views
Creating intergenic bam file
R
genome
intergenic
alignment
7.7 years ago by
erincyurtman
• 0
2
votes
17
replies
4.4k
views
Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
sam
bam
alignment
samtools
updated 10.3 years ago by
Devon Ryan
104k • written 10.3 years ago by
Rohit
★ 1.5k
3
votes
17
replies
1.5k
views
copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
CNV
DownSample
fastq
copy number not accurate
4.2 years ago by
lffu_0032
▴ 90
1
vote
17
replies
2.4k
views
Normalizing BLAST results
blast
updated 6.6 years ago by
Biostar
20 • written 6.7 years ago by
db
• 0
8
votes
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools
relatedness
6.2 years ago by
Sharon
▴ 600
3
votes
17
replies
2.8k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing
faire
mapping
3.1 years ago by
boczniak767
▴ 850
0
votes
17
replies
2.7k
views
Fail running blastdb and blastn on my own computer
blast
6.5 years ago by
annette440
• 0
0
votes
17
replies
1.5k
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
3.6 years ago by
Dunois
★ 2.5k
2
votes
17
replies
9.6k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping
genome
fastq
STAR
updated 2.1 years ago by
todd.ugine
• 0 • written 3.3 years ago by
merfer0206
• 0
4
votes
17
replies
2.8k
views
Cufflinks analysis and gffread
RNA-Seq
Assembly
updated 6.5 years ago by
Kevin Blighe
87k • written 6.5 years ago by
qudrat
▴ 100
7
votes
17
replies
6.5k
views
HeatMap: how to cluster only the rows and keep order of the heatmap's column labels as same as in the df?
R
gene
genome
5.8 years ago by
WUSCHEL
▴ 750
0
votes
17
replies
1.1k
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
3 months ago by
Foad
▴ 10
0
votes
17
replies
3.1k
views
I am not able to let R read my file
R
fasta
updated 3.1 years ago by
Arup Ghosh
3.2k • written 3.1 years ago by
trejomarco6
• 0
2
votes
17
replies
5.1k
views
Coding Potential Calculator (CPC) error
RNA-Seq
updated 6.1 years ago by
h.mon
35k • written 6.1 years ago by
Janey
▴ 30
1
vote
17
replies
5.7k
views
BBMap: Mapping Fails
BBTools
BBMap
Mapping
updated 8.1 years ago by
GenoMax
141k • written 8.1 years ago by
cacampbell
▴ 60
7
votes
16
replies
3.6k
views
How do I get a GFF file
snp
4.8 years ago by
apl00028
▴ 90
0
votes
16
replies
4.6k
views
Issue using MaSuRCA-3.2.6
Assembly
assembler
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
Chvatil
▴ 130
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 10 months ago by
Ram
43k • written 4.2 years ago by
Ankit
▴ 500
3
votes
16
replies
3.5k
views
FastTree trifurcating Root node
alignment
FastTree
Phylogenetic Tree
5.3 years ago by
Moses
▴ 150
2
votes
16
replies
3.1k
views
Enhancing draft genome using 10X data
10X
draft_genome
Assembly
5.7 years ago by
Mostafa
▴ 20
7
votes
16
replies
2.8k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq
sequencing
updated 13 months ago by
Ram
43k • written 6.5 years ago by
Matteo Schiavinato
★ 3.6k
4
votes
16
replies
8.7k
views
STAR - genome indexes generation, genome file not created
RNA-Seq
star
updated 4.6 years ago by
Biostar
20 • written 7.4 years ago by
lu.ne
▴ 70
5
votes
16
replies
2.6k
views
a lot of OTUs wth no reference
16S
6.5 years ago by
agata88
▴ 870
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene
next-gen
4.3 years ago by
Chaimaa
▴ 260
9
votes
16
replies
1.9k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
5.5 years ago by
bioinfo456
▴ 150
0
votes
16
replies
4.3k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 21 months ago by
Ram
43k • written 9.0 years ago by
bharata1803
▴ 560
1,000 results • Page
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Recent Votes
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)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
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