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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
2
votes
18
replies
2.8k
views
Bwa on multiple processor
np
mpirun
bwa
alignment
2.3 years ago by
shivangi.agarwal800
▴ 120
3
votes
18
replies
3.2k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 2.8 years ago by
Ram
43k • written 2.8 years ago by
Nai
▴ 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
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
4
votes
18
replies
3.0k
views
Inline barcodes in the reverse reads
barcodes
7.5 years ago by
Picasa
▴ 640
7
votes
18
replies
4.9k
views
Fold change UP and Down in dplyr calculation
R
6.7 years ago by
1769mkc
★ 1.2k
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
26 days ago by
b.contreras.moreira
▴ 170
7
votes
18
replies
8.6k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
hana
▴ 190
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
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
5
votes
17
replies
4.3k
views
Interpreting Genome_Structural_Correction Block_Bootstrap.Py
statistics
encode
10.2 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
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
6.6 years ago by
anonymous1192976466
▴ 50
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
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
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
8
votes
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools
relatedness
6.2 years ago by
Sharon
▴ 600
1
vote
17
replies
4.2k
views
Error executing bedops convert2bed
bedops
bed
vcf
convert2bed
7.3 years ago by
lakhujanivijay
5.8k
0
votes
17
replies
2.8k
views
Fail running blastdb and blastn on my own computer
blast
6.5 years ago by
annette440
• 0
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
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
16
votes
17
replies
3.2k
views
6 follow
RNA seq pipeline
RNA-Seq
6.5 years ago by
dimitrischat
▴ 210
3
votes
17
replies
1.6k
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
2
votes
17
replies
9.7k
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
9
votes
17
replies
2.2k
views
Creating intergenic bam file
R
genome
intergenic
alignment
7.7 years ago by
erincyurtman
• 0
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
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
4
votes
17
replies
2.9k
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
20
votes
17
replies
3.3k
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
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
2
votes
17
replies
2.9k
views
Snakemake Megahit error
megahit
Snakemake
2.5 years ago by
blackadder
▴ 30
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
6
votes
17
replies
2.4k
views
6 follow
Issue with reverting bam file back to fastq files
next-gen
assembly
genome
alignment
5.9 years ago by
williamsbrian5064
▴ 510
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
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
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
0
votes
17
replies
1.1k
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
3 months ago by
Foad
▴ 10
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 4.3 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
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
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 7.4 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
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
1,000 results • Page
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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: 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
noodle
▴ 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
Gordon Smyth
★ 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…
Comment: PDB related issue
by
noodle
▴ 550
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…
Comment: PDB related issue
by
Mensur Dlakic
★ 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…
Answer: NGS forensics: how to know if data is fabricated
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…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
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