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1,000 results • Page
4 of 20
Sort: replies
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Views
Votes
Replies
13
votes
16
replies
6.1k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon
mask
trimming
fastq
7.3 years ago by
Paul
★ 1.5k
15
votes
16
replies
1.7k
views
ncbi error report log for validate fastq issue
sra-tools
updated 7 months ago by
GenoMax
141k • written 7 months ago by
1769mkc
★ 1.2k
5
votes
16
replies
2.6k
views
a lot of OTUs wth no reference
16S
6.5 years ago by
agata88
▴ 870
4
votes
16
replies
1.8k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
updated 9 weeks ago by
Ram
43k • written 7 months ago by
ella
• 0
5
votes
16
replies
6.2k
views
Remove duplicate lines based on specific columns
r
python
intersect
reads
updated 5.6 years ago by
Ram
43k • written 5.6 years ago by
dzisis1986
▴ 70
7
votes
16
replies
3.6k
views
How do I get a GFF file
snp
4.9 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
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 6.6 years ago by
Matteo Schiavinato
★ 3.6k
2
votes
16
replies
1.9k
views
I want to know is it a true method ?
vcf
SNP
realignment
6.1 years ago by
Siavash Salek Ardestani
▴ 20
1
vote
16
replies
2.7k
views
Merging fastq files from two experiments
FASTQ
NGS
updated 5.2 years ago by
Biostar
20 • written 5.3 years ago by
zizigolu
★ 4.3k
9
votes
16
replies
3.8k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 13 months ago by
Ram
43k • written 5.7 years ago by
marongiu.luigi
▴ 710
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 4.3 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
9
votes
16
replies
1.5k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.7 years ago by
lieven.sterck
15k • written 3.7 years ago by
schlogl
▴ 160
4
votes
16
replies
8.7k
views
STAR - genome indexes generation, genome file not created
RNA-Seq
star
updated 4.7 years ago by
Biostar
20 • written 7.5 years ago by
lu.ne
▴ 70
5
votes
16
replies
4.3k
views
plotting problem with loop in R
R
plot
4.9 years ago by
smyiz
▴ 30
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
2
votes
16
replies
10k
views
Tophat with Bowtie2 long index
tophat
bowtie
updated 2.3 years ago by
Ram
43k • written 9.8 years ago by
BDK_compbio
▴ 140
0
votes
16
replies
3.8k
views
Gff to genbank - feature is missing
DNA
augustus
gff3
genbank
updated 11 months ago by
Ram
43k • written 5.9 years ago by
rororo
▴ 10
13
votes
16
replies
7.2k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa
samtools
mpileup
5.3 years ago by
DNAngel
▴ 250
0
votes
16
replies
4.3k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 22 months ago by
Ram
43k • written 9.0 years ago by
bharata1803
▴ 560
1
vote
16
replies
2.0k
views
Why I see very high mapping percentage, Is this normal or anything wrong in generating libraries?
RNA-Seq
hisat2
samtools
mapping
updated 5.9 years ago by
Biostar
20 • written 6.0 years ago by
Vasu
▴ 770
7
votes
16
replies
3.9k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing
genome-sequence
fastqc
genome
sequence
4.1 years ago by
Researcher
▴ 20
0
votes
16
replies
5.2k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools
sort
10.9 years ago by
chentong.biology
▴ 50
3
votes
16
replies
1.6k
views
Problem, getting information only from the last row and not from all the rows
perl
6.0 years ago by
ArusjakGevorgyan
▴ 30
16
votes
16
replies
3.2k
views
Using DESeq2 results for building a classifier
deseq2
RNA-Seq
differentially expressed genes
6.1 years ago by
bioinfo456
▴ 150
0
votes
15
replies
2.1k
views
Chromosome accession numbers correspond to which chromosome?
bam
chromosome
bed
18 months ago by
amy__
▴ 160
4
votes
15
replies
3.3k
views
Adding Multiple readgroups to BAM file
GATK
ReadGroups
8.0 years ago by
vakul.mohanty
▴ 270
0
votes
15
replies
3.2k
views
SAMFormatException: Did not inflate expected amount error
WES
updated 2.5 years ago by
greekkey
▴ 20 • written 2.8 years ago by
smrutimayipanda
▴ 20
2
votes
15
replies
4.1k
views
Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
next-gen
SNP
alignment
updated 4.1 years ago by
wm
▴ 560 • written 4.1 years ago by
shrutidabral
▴ 10
7
votes
15
replies
2.2k
views
very low coverage when mappin genomic DNA
mapping
coverage
DNA
genomic
updated 2.7 years ago by
ATpoint
82k • written 2.7 years ago by
Lila M
★ 1.2k
5
votes
15
replies
2.2k
views
Is this a valid analysis?
geo
rankprod
analysis
microarray
7.5 years ago by
randalljellis
▴ 90
1
vote
15
replies
1.6k
views
Single Cell RNA Seq
scTransform
Harmony
scRNAseq
Seurat
8 months ago by
scRNA2023
• 0
3
votes
15
replies
3.2k
views
Less and less genes predicted with each iteration of SNAP/MAKER
maker
annotation
snap
gene prediction
genomics
updated 2.6 years ago by
jaredbernard
▴ 20 • written 4.1 years ago by
mrmrwinter
▴ 30
2
votes
15
replies
1.6k
views
from protein to tRNA combinations
RNA-Seq
rna-seq
written 3.4 years ago by
shiningsky000
• 0
1
vote
15
replies
3.3k
views
How to perform multiple alignment using MAFFT?
genome
alignment
gene
sequence
3.0 years ago by
anikcropscience
▴ 230
6
votes
15
replies
1.6k
views
The Best Cloud Solution For Genomics
cloud
data-sharing
genomics
workflow
updated 21 months ago by
Ram
43k • written 22 months ago by
davidmaimoun
▴ 50
3
votes
15
replies
2.8k
views
fastq reads with primers and truseq indexed adapter
sequencing
next-gen
sequence
7.1 years ago by
jomo018
▴ 720
2
votes
15
replies
4.2k
views
How to interpret reads mapped to genome from samtools flagstat vs TopHat align_summary.txt ?
RNA-Seq
8.0 years ago by
Vasu
▴ 770
5
votes
15
replies
2.1k
views
Sample contamination level over 30%
next-gen
6.6 years ago by
haiying.kong
▴ 360
1
vote
15
replies
3.6k
views
Install Lefse in Ubuntu 12
install
lefse
microbiome
5.9 years ago by
goh
▴ 10
5
votes
15
replies
1.9k
views
Testing uniform distribution of SNPs across chromosome
uniform
vcf
SNP
5.0 years ago by
misterie
▴ 110
0
votes
15
replies
3.7k
views
Identify genes in a tophat aligned bam/sam file
blast
alignment
rna-seq
gene
updated 16 months ago by
Ram
43k • written 8.9 years ago by
gchaves
• 0
0
votes
15
replies
3.3k
views
how to make a .bam file from fastQ for RNA-seq ion torrent with BBmap
RNA-Seq
6.6 years ago by
genya35
▴ 40
10
votes
15
replies
6.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 13 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
11
votes
15
replies
2.8k
views
How do I get the read counts for a specific exon
bam
exon
updated 6.1 years ago by
Ram
43k • written 6.1 years ago by
b10hazard
▴ 30
1
vote
15
replies
2.8k
views
Copy Number Analysis on single file
CNV
updated 4.7 years ago by
Kevin Blighe
87k • written 4.7 years ago by
user31888
▴ 130
1
vote
15
replies
4.4k
views
Ultrafast alignment of short sequences to a genome (with up to 5 mismatches!)
genome
alignment
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Aurelie MLB
▴ 360
1,000 results • Page
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The Biostar Herald for Monday, April 29, 2024
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Comment: Landmark gene selection in L1000.
by
kim
• 0
thank you for reply, but i want some information for what microarray data are selected for L1000. thank you!
Answer: Why cd-hit-est not work when sequence identity threshold<0.95?
by
weidonglu
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The reason for your problem was most likely due to you relative complex data and too little system memory. For 20000-30000 transcriptome se…
Comment: Perfom a Gene Ontology Analysis from GO terms txt file
by
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Your table should look like this (GO terms): ``` geneid GOid Zm00001eb000010 GO:0003690;GO:0003727;GO:0019843;GO:0005739 Zm00001eb000020 G…
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I understand, here is an example with topGO where you need a differential expression table (DESeq2 for example) and a table of GO terms: `…
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by
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Thank u for your reply. The problem is that I used the genome and gene annotation from that webpage, not ensemble or ncbi, so I have to use…
Comment: Perfom a Gene Ontology Analysis from GO terms file
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Hello, To perform functional enrichment analysis there are packages such as topGO or clusterProfiler that can work very well. Lately I've …
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The anti-diagonal band does suggest some fraction of genotypes are strand-flipped - probably G/C or A/T variants.
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Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
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Thank you! I need this for eukaryotic organism and known protein sequences, but I guess seqkit would work well!
Comment: Landmark gene selection in L1000.
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Paper referred to in question: https://pubmed.ncbi.nlm.nih.gov/29195078/ > so I want to understand how you reduced the 12063 genes to 978…
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Protein attribute prediction
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@kevin May I know whether your comments and edits were mainly based on the fact that "Previously, [crazy] people had been using the origina…
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Wow, I was shocked at this AI answer that looks to be a good start for using UniProt. Sharing it in case it is useful. (It will work in ses…
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> Can you clarify what you mean by "100% of reads pass cutadapt, even > though 70% of reads contain adapters and get trimmed. The header o…
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If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
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