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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
2
votes
12
replies
4.1k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 6 weeks ago by
Ram
38k • written 7.9 years ago by
cmogren
▴ 20
0
votes
12
replies
833
views
Can't exec "cd": No such file or directory at ./PAst.pl line 43
PAst
updated 10 months ago by
lieven.sterck
14k • written 10 months ago by
Neel
▴ 10
3
votes
12
replies
3.5k
views
Chromosome Data -- Only genes for given chromosome, without introns and with annotated motifs, possible?
Assembly
gene
sequence
genome
rna-seq
updated 12 months ago by
Ram
38k • written 8.2 years ago by
ldpubsec
▴ 80
1
vote
12
replies
3.5k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 10 weeks ago by
ATpoint
70k • written 5.5 years ago by
SMILE
▴ 170
5
votes
12
replies
518
views
Data from an experiment
single-cell
updated 5 weeks ago by
GenoMax
127k • written 5 weeks ago by
Chris
▴ 70
0
votes
12
replies
2.0k
views
Tax4Fun2 - error
tax4fun
silva
blast
updated 7 months ago by
GenoMax
127k • written 13 months ago by
ymj
▴ 10
1
vote
12
replies
3.1k
views
How to run multiple alignment and SNP-calling of WGS data in .gb and .fasta using Python or Ruby/Java or any free software?
alignment
sequencing
software
updated 9 months ago by
Ram
38k • written 8.0 years ago by
fashiondesignrussian
▴ 60
6
votes
12
replies
1.1k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 4 days ago by
Ram
38k • written 4.2 years ago by
english.server
▴ 290
1
vote
12
replies
655
views
weird alignment results for RNAseq data
hisat2
star
updated 11 months ago by
cpad0112
21k • written 11 months ago by
Sara
▴ 220
2
votes
12
replies
1.2k
views
The best way to get gene lengths for 15K+ genes?
r
EDAseq
RNA-seq
5 months ago by
JACKY
▴ 80
0
votes
12
replies
3.5k
views
Problem: kmergenie has a minimum number of input of reads?
K-mers
Kmergenie
updated 10 months ago by
Ram
38k • written 8.1 years ago by
Leandro de Mattos
▴ 90
2
votes
12
replies
1.8k
views
Nothing will align with HTSeq?
RNA-Seq
htseq
updated 6 months ago by
Ram
38k • written 7.5 years ago by
Kristin Muench
▴ 610
0
votes
12
replies
2.6k
views
Allpaths- Keep getting ConvertToFastbQualb.pl failed for group 'paired_ends' when I run PrepareAllPaths
next-gen
Assembly
updated 3 months ago by
Ram
38k • written 7.7 years ago by
mafireyi
▴ 80
6
votes
12
replies
1.2k
views
VCF files 101 - for people from non Bioinformatics Background
vcf
sequencing
genome
variant-calling
updated 8 days ago by
Ram
38k • written 2.6 years ago by
akshaykum684
▴ 20
0
votes
12
replies
893
views
Splitting CRAM files
CRAM-files
sequence-alignment
3 months ago by
langziv
▴ 20
1
vote
12
replies
3.1k
views
dN/dS analysis of genomes
genome
sequence
alignment
5 months ago by
Mehmet
▴ 790
4
votes
12
replies
899
views
Bulk RNA seq: all p adjusted are the same
p-adj
RNA-seq
differential-gene-expression
updated 12 weeks ago by
Ram
38k • written 10 months ago by
nils.simon.biology
▴ 10
8
votes
12
replies
2.4k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 4 days ago by
Ram
38k • written 19 months ago by
daver.v
▴ 30
5
votes
11
replies
3.0k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 7 days ago by
Ram
38k • written 4.9 years ago by
HG
▴ 30
1
vote
11
replies
4.0k
views
Running survival analysis using Rplink
Cox
Survival
R
GWAS
PLINK
updated 11 months ago by
Ram
38k • written 8.2 years ago by
Caragh
▴ 40
1
vote
11
replies
2.9k
views
bedtools fisher interpretation of "in -a" "not in -b"
fisher
bedtools
intersection
updated 4 weeks ago by
Ram
38k • written 5.1 years ago by
jomo018
▴ 690
4
votes
11
replies
1.0k
views
Running STAR
STAR
7 months ago by
Chris
▴ 70
0
votes
11
replies
1.2k
views
Error in Importing data in qiime2
Metagenomics
Sequencing
Qiime2
Amplicon
8 months ago by
Vaishnavi
• 0
0
votes
11
replies
2.3k
views
mpiBLAST Score and E-value Calculation
blast
sequence
updated 9 months ago by
Ram
38k • written 8.0 years ago by
Lakshman Rao
• 0
1
vote
11
replies
2.8k
views
merge samples in phyloseq returns NAs
R
phyloseq
biom
updated 4 months ago by
joe.e.weaver
• 0 • written 2.7 years ago by
annaA
▴ 10
4
votes
11
replies
2.3k
views
7 follow
Getting coding sequence length
NCBI
Gene
CDS
updated 9 months ago by
newbio17
▴ 350 • written 2.7 years ago by
fi1d18
★ 4.1k
3
votes
11
replies
12k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq
RNA-Seq
STAR
updated 11 months ago by
Ram
38k • written 8.2 years ago by
noushin.farnoud
▴ 120
5
votes
11
replies
6.3k
views
Error while running miso
RNA-Seq
splicing
updated 7 months ago by
Ram
38k • written 7.6 years ago by
priyankamaripuri
▴ 40
3
votes
11
replies
992
views
Feature count is very low using htseq-count
htseq
bbmap
11 months ago by
salmon
▴ 10
4
votes
11
replies
2.6k
views
Please add an explicit type tag :NAME
software-error
next-gen
genome
updated 7 weeks ago by
Ram
38k • written 4.9 years ago by
mahdikhadem95
▴ 30
8
votes
11
replies
1.2k
views
using STAR instead of HISAT2
STAR
updated 7 months ago by
Ram
38k • written 7 months ago by
Chris
▴ 70
0
votes
11
replies
751
views
Problem with Trimmomatic Multiple Paired-End sequencing.
Trimmomatic
updated 8 weeks ago by
GenoMax
127k • written 9 weeks ago by
john
• 0
10
votes
11
replies
8.2k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 9 months ago by
Ram
38k • written 8.0 years ago by
SheelS
▴ 40
6
votes
11
replies
686
views
Calculate RPKM
RPKM
1 day ago by
Chris
▴ 70
3
votes
11
replies
781
views
RepeatMasker error
repeatmasking
transciptome
RNA-seq
updated 8 months ago by
mark.ziemann
★ 1.8k • written 8 months ago by
barrypraveen
▴ 100
4
votes
11
replies
5.6k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
7 months ago by
prasundutta87
▴ 650
0
votes
11
replies
795
views
Python - Samtools mpileup find snps with allele frequency
snp
mpileup
python
samtools
8 months ago by
pablosolar.r
▴ 20
3
votes
10
replies
3.1k
views
Somaticsniper Hangs Up
updated 11 months ago by
Ram
38k • written 9.1 years ago by
Jack
▴ 80
0
votes
10
replies
745
views
using txt file to pass pathways for pipelines
muscle
seqkit
bash
fasta
updated 8 months ago by
Ram
38k • written 8 months ago by
Hugo
• 0
2
votes
10
replies
5.9k
views
fq.gz file use
BioEdit
R
updated 4 days ago by
Ram
38k • written 4.1 years ago by
choi.yisoo.hi
• 0
5
votes
10
replies
4.5k
views
Antisense transcription - how to detect it?
RNA-Seq
antisense
updated 6 months ago by
Ram
38k • written 7.4 years ago by
John
13k
2
votes
10
replies
683
views
R-studio freezes error
RStudio
offtopic
updated 5 months ago by
Ram
38k • written 5 months ago by
Amr
▴ 140
0
votes
10
replies
966
views
DeSeq2 "some values in assay are negative"
RNAseq
4 months ago by
Morris_Chair
▴ 330
3
votes
10
replies
980
views
how to delete a file 3 months after downloading it in python
python
pandas
updated 10 months ago by
ATpoint
70k • written 21 months ago by
Debut
▴ 20
3
votes
10
replies
731
views
Error with FindConservedMarkers()
FindConservedMarkers
5 weeks ago by
Chris
▴ 70
4
votes
10
replies
355
views
Extract unmapped reads OR reads covering chromosome 6 from a bam file?
fastq
bam
samtools
picard
5 weeks ago by
dps2501
▴ 20
1
vote
10
replies
1.0k
views
The modules are not clustered together after WGCNA
cluster
WGCNA
r
dendrograms
10 months ago by
cwwong13
▴ 20
0
votes
10
replies
6.6k
views
Error: reads file does not look like a fastq file
fastq
bowtie2
ChIP-Seq
updated 4 days ago by
Ram
38k • written 6.5 years ago by
addilynn.beach
▴ 40
1
vote
10
replies
2.3k
views
Issue in running viroBlast from localhost
blast
php
viroBlast
javascript
sequence
updated 8 months ago by
Ram
38k • written 7.1 years ago by
arfaj a
▴ 10
5
votes
10
replies
671
views
How to change chromosome names in assembly fasta downloaded from NCBI?
grch38
ncbi
grch37
fasta
6 months ago by
magnolia
▴ 20
1,000 results • Page
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Comment: getting coding exon information from Ensembl API
C: How to install TMAP
If there is a way to link two gosling html components in two <div>s.
A: Using GATK's HaplotypeCaller or Mutect2 for somatic cancer samples with no norma
Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
Comment: Where do find virulence gene information in a gff/gtf file?
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Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
Juke34
7.7k
Don't use `--merge_loci` in your command line this was for AGAT version <1.0.0 (and only few scripts), now this is handled via the config.y…
Comment: getting coding exon information from Ensembl API
by
Ram
38k
> Because you just answer No we don't. I think you're confusing this professional forum contributed to by volunteers with a customer suppo…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
Ram
38k
Oh, you can just use TPM to do that. Within sample comparison is a completely different (and much easier) game.
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
by
Sian
• 0
Unfortunately yes, there does seem to be a problem with using the older version - when I came to do more analysis yesterday, the enrichKEGG…
Comment: getting coding exon information from Ensembl API
by
Sarah
▴ 30
Because you just answer when it's a stupid question or when I ask a lot of questions. This is for asking questions not for being judged by …
Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
by
Manav
• 0
Thanks, tried working with the dataset and workflow. It worked.
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
BioinfoBee
• 0
@juke34 Thanks again. I changed the config.yaml *should overlapping loci (at CDS level) be merged in a single locus Only one gene is kept,…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
Thanks, I am not doing any differential. But, Can we say that 6th transcript is relatively more abundance in our sample than other transcri…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
zrm22
▴ 30
It looks like the ImputePipelinePlugin for the minimap2 run does not use the numThreads Option but rather does the numThreadsOnMachine - 2 …
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
@rob Please, Can you or people from your group answer . As I am using one of your paper as my [reference.][1] [1]: https://f1000rese…
Comment: fastq_screen error: Failed to calculate read length
by
firestar
★ 1.5k
I created the .fasta from a BAM, so I am just going to go back to the BAM and convert that to a .fastq and see if that works. But good to k…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
Ram
38k
> I have only one condition There is no "differential" then. RNAseq is a relative measure, so comparing single-condition replicates using …
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
[Salmon][1] is giving me TPM at transcript level. So, What I understand from that TPM is normalized for sequencing depth and Transcript l…
Answer: Does it possible to know what are the adjacent genes up to 1000bp upstream and
by
Alex Reynolds
34k
You could use `bedmap` from BEDOPS. Say you have a BED file of IS/transposable elements called `elements.bed` and a BED file of genes calle…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
twrl8
• 0
Ahh thank you! I thought the xmx parameter would be passed to the downstream commands called by the plugin. Then I think I definitely need…
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