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1,000 results • Page
4 of 20
Sort: replies
Rank
Views
Votes
Replies
5
votes
16
replies
2.7k
views
How to extract intron counts from total RNA Sequencing?
featurecounts
RNAseq
htseq
STAR
17 months ago by
PK
▴ 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 4.3 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
0
votes
16
replies
2.8k
views
How to convert ncbi gff file to ensembl gff format
bcftools
gff
updated 13 months ago by
Ram
43k • written 20 months ago by
yoser4
▴ 10
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
5
votes
16
replies
2.6k
views
a lot of OTUs wth no reference
16S
6.5 years ago by
agata88
▴ 870
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
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
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
0
votes
16
replies
5.2k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools
sort
11.0 years ago by
chentong.biology
▴ 50
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
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
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
1
vote
16
replies
7.0k
views
After sorting bam file not able to index ?
alignment
next-gen
updated 5.2 years ago by
Biostar
20 • written 5.3 years ago by
sunnykevin97
▴ 980
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
0
votes
16
replies
3.2k
views
Problems with installation of Prodege decontamination software
genome
next-gen
sequencing
sequence
blast
updated 7.2 years ago by
Biostar
20 • written 7.3 years ago by
tans0307
• 0
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
4
votes
16
replies
6.1k
views
How to count occurrence of numbers in text files using phython
python
excel
counting
writelines
7.3 years ago by
Kachibunny
• 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
14
votes
16
replies
2.0k
views
Why are some mapped reads not mapped completely?
RNA-Seq
mapping
updated 3.5 years ago by
lieven.sterck
15k • written 3.5 years ago by
utsafar
▴ 80
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
7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
7.7 years ago by
aggregatibacter
▴ 180
4
votes
16
replies
4.5k
views
Working with human database in Kraken
RNA-Seq
next-gen
genome
7.9 years ago by
Ron
★ 1.2k
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Star
▴ 60
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
15
replies
3.7k
views
Can I use PICARD (SortSam) instead of SAMTOOLS (sort) for sorting bam files in RNAseq pipeline where HISAT2 is used for alignment.
RNA-Seq
software error
sequencing
next-gen
6.0 years ago by
shuksi1984
▴ 60
0
votes
15
replies
2.0k
views
compare two NCBI ftp tables
table
NCBI
updated 2.9 years ago by
Ram
43k • written 2.9 years ago by
Debut
▴ 20
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
8
votes
15
replies
2.0k
views
RNAseq differential expression analysis : no significative FDR but significative GO enrichment
RNA-Seq
differential expression
4.5 years ago by
guillaume.rbt
★ 1.0k
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
1
vote
15
replies
3.7k
views
Fastx quality filter
next-gen
RNA-Seq
software error
sequencing
updated 7.4 years ago by
Ram
43k • written 7.4 years ago by
kriti.awasthi23
▴ 10
2
votes
15
replies
1.5k
views
How to call all the allele in samples
SNP
6.0 years ago by
Kritika
▴ 260
3
votes
15
replies
2.0k
views
Overlapping regions in a BED file
regions
BED
Sequence
exons
annotation
22 months ago by
Matej
• 0
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
0
votes
15
replies
2.4k
views
pathway analysis tools for xenopus
pathways
omics
xenopus
updated 7.8 years ago by
EagleEye
7.5k • written 7.8 years ago by
mike
▴ 90
7
votes
15
replies
7.1k
views
6 follow
blastn error - NCBI C++ Exception
assembly
blast
alignment
updated 2.1 years ago by
lieven.sterck
15k • written 3.1 years ago by
sunnykevin97
▴ 980
1
vote
15
replies
1.5k
views
How to reduce my dataset in order to plot it?
correlation
igraph
updated 4.7 years ago by
Biostar
20 • written 4.9 years ago by
pablo
▴ 300
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
6
votes
15
replies
1.6k
views
Reads partly within an exon
RNA-Seq
6.8 years ago by
benjyrolls
▴ 70
2
votes
15
replies
1.1k
views
Manipulate refseq database
ncbi
database
nt
refseq
updated 4.2 years ago by
Biostar
20 • written 4.3 years ago by
anasofiamoreira94
▴ 80
1
vote
15
replies
6.0k
views
How to Extract Specific Region on Bam file
Nanopore
HG38
Rna-Seq
Genome
updated 2.9 years ago by
Kevin Blighe
87k • written 2.9 years ago by
santos48
▴ 40
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
8.4k
views
Strand specific protocol for bowtie2 alignment
bowtie2
rnaseq
alignment
RNA-Seq
updated 2.5 years ago by
Ram
43k • written 8.5 years ago by
nalandaatmi
▴ 100
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling
bcftools
nf-core
10 months ago by
Chris
▴ 260
2
votes
15
replies
2.2k
views
to get each covariate with PC loading in PCA
RNA-seq
PCA
5.3 years ago by
Grace_G
▴ 20
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
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
4 of 20
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A: Decoy In Reference Assembly
Decoy In Reference Assembly
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Comment: Bacterial plasmid analysis
Unsupervised clustering on gene expression data
Answer: Bacterial plasmid analysis
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Recent Replies
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
GenoMax
142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA)
by
ATpoint
82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
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82k
DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
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In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA)
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Thank you @atpoint, I did already investigate this error on the DADA2 github. It seems that the "BiocParallel" error can be due to multipl…
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Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
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One cannot help you with this. The error is from R, yet you show not a single line of R code.
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I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequenc…
Comment: Subsetting and merging back Seurat Object brings different results
by
Bine
▴ 60
Ok I think I know what happened. The order of cells changed, otherwise its the same: ![image](https://github.com/satijalab/seurat/assets/7…
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8.5k
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I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
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by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
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