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1,000 results • Page
4 of 20
Sort: replies
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Views
Votes
Replies
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
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
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
3
votes
16
replies
4.1k
views
GC content of 10x Genomics
fastqc
10x
GC content
updated 3.7 years ago by
Eugene A
▴ 180 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
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
5
votes
16
replies
2.6k
views
a lot of OTUs wth no reference
16S
6.5 years ago by
agata88
▴ 870
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
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
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
7.7 years ago by
aggregatibacter
▴ 180
4
votes
16
replies
977
views
hisat2 location does not exist
hisat2
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Eric
• 0
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
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
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
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
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
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
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
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
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
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
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
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
3
votes
15
replies
5.6k
views
Pairwise sequence alignment with Biojava?
sequence-alignment
biojava
java
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
Bioaln
▴ 360
2
votes
15
replies
4.6k
views
Error when indexing a bcf file
vcf
bcf
5.7 years ago by
Famf
▴ 30
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
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
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
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
2.6k
views
Strategy for generating a consensus sequence for 100 complete bacterial genomes?
consensus seq
mauve
5.8 years ago by
Alec Watanabe
▴ 60
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
3.3k
views
How to perform multiple alignment using MAFFT?
genome
alignment
gene
sequence
3.0 years ago by
anikcropscience
▴ 230
2
votes
15
replies
1.5k
views
How to call all the allele in samples
SNP
6.0 years ago by
Kritika
▴ 260
6
votes
15
replies
2.5k
views
processing in strelka2 with multiples bam file in directory
strelka2
updated 2.3 years ago by
aldhairmedico
▴ 70 • written 4.4 years ago by
bioguy24
▴ 230
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
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
6.5 years ago by
genya35
▴ 40
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
5 months ago by
analyst
▴ 30
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
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
5
votes
15
replies
5.4k
views
Annotation with snpEFF
annotation
vcf
snpeff
extractFields
updated 5.8 years ago by
Biostar
20 • written 5.9 years ago by
NB
▴ 960
1,000 results • Page
4 of 20
Recent Votes
Comment: PDB related issue
Comment: PDB related issue
Comment: NGS forensics: how to know if data is fabricated
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
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Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
I reinstalled nodejs: > sudo apt-get install nodejs Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated
by
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▴ 270
Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 550
Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated
by
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▴ 550
I'm a bit against pubpeer - have you ever posted there? My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
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★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
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You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
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★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
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by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
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