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832 results • Page
2 of 17
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Views
Votes
Replies
1
vote
9
replies
3.5k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 14 hours ago by
Ram
43k • written 17 months ago by
Manav
• 0
4
votes
12
replies
3.4k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 2 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
3
votes
7
replies
3.4k
views
WGCNA adjust p value
statistics
WGCNA
updated 14 days ago by
Ceren
• 0 • written 2.7 years ago by
jason.taotaotan
▴ 10
2
votes
6
replies
3.3k
views
Base Quality of a reported variant in VCF
alignment
FASTQ
VCF
next-gen
Variant-Calling
updated 2 days ago by
Ram
43k • written 9.1 years ago by
VineethVenumadhavan
▴ 50
4
votes
2
replies
3.3k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 3 days ago by
vague-barracuda-4686
• 0 • written 16 months ago by
shinyjj
▴ 50
75
votes
19
replies
3.3k
views
11 follow
Blog:
A list of technical advantages of Snakemake over Nextflow | Cloud solution for Snakemake
Snakemake
updated 27 days ago by
LauferVA
4.1k • written 6 months ago by
Kenny
▴ 30
7
votes
7
replies
3.3k
views
How to perform normalization when converting ATAC bam file to bigwig file using deeptools for IGV visualization
bamCoverage
deeptools
bigwig
IGV
ATAC
updated 6 days ago by
sgv
• 0 • written 2.2 years ago by
sir.outman
▴ 40
1
vote
8
replies
3.2k
views
cutadapt error problem
next-gen
cutadapt
updated 16 hours ago by
Ram
43k • written 5.5 years ago by
amitpande74
▴ 20
0
votes
3
replies
3.0k
views
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
R
next-gen-sequencing
absolute
updated 16 hours ago by
Ram
43k • written 6.7 years ago by
namhaesly
• 0
6
votes
10
replies
2.7k
views
How can Investigate if a Viral genome is circular or linear? And if it is single or double stranded?
Assembly
genome
updated 27 days ago by
Israel
• 0 • written 5.3 years ago by
GiV17
▴ 50
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 3 days ago by
axol0tl
• 0 • written 6.4 years ago by
Xinwei Han
• 0
5
votes
2
replies
2.5k
views
Tool:
Coovar: Co-Occurring Variant Analyzer
snp
variant-annotation
updated 21 days ago by
GenoMax
140k • written 11.4 years ago by
Christian
★ 3.0k
2
votes
1
reply
2.5k
views
CRAM reference registry and the GRch38 reference genome
BAM
Samtools
GRCh38
CRAM
Variant-Calling
updated 2 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
1
vote
6
replies
2.4k
views
Variant calling from multiple sequencing runs for a single samples
variant-calling
updated 2 days ago by
Ram
43k • written 6.9 years ago by
harish.nucl
• 0
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq
Somatic-Mutation
Variant-Calling
updated 2 days ago by
Ram
43k • written 6.1 years ago by
Sharon
▴ 600
1
vote
3
replies
2.4k
views
How to remove variants with 3+ alleles present Plink1.9
HaplotypeCaller
GATK
Plink1.9
vcftools
updated 7 days ago by
Jingjingzhang
• 0 • written 2.1 years ago by
ramshahaya
▴ 10
12
votes
14
replies
2.4k
views
8 follow
Forum:
Recovering bam files after unknown deletion in the storage
photorec
bam
sequencing
written 4.8 years ago by
Gabriel Wajnberg
▴ 70
6
votes
3
replies
2.3k
views
ChipQC doesn't run
ChIP-Seq
updated 14 days ago by
armando_c2
• 0 • written 4.1 years ago by
francesca3
▴ 140
2
votes
5
replies
2.3k
views
GTF file for HIV strain pNL4-3
HIV
annotation
mapping
updated 28 days ago by
xiaoleiusc
▴ 140 • written 5.8 years ago by
caggtaagtat
★ 1.8k
5
votes
4
replies
2.3k
views
How to call mitochondrial SNP?
SNP
mitochondrial
updated 24 days ago by
Ram
43k • written 6.9 years ago by
hxlei613
▴ 100
0
votes
1
reply
2.3k
views
Segmentation fault for cd-hit
software-error
updated 19 days ago by
GenoMax
140k • written 9.0 years ago by
Crystal
▴ 70
5
votes
8
replies
2.2k
views
VariantCalling with single sanger read
snps
blast
indel
Variant-Calling
updated 2 days ago by
Ram
43k • written 7.6 years ago by
Amirosein
▴ 70
0
votes
3
replies
2.2k
views
ANGeS - Ancestral Genome reconstruction
ancestral
genome
updated 21 days ago by
illodukarthickbabu
• 0 • written 2.6 years ago by
alslonik
▴ 310
3
votes
2
replies
2.2k
views
Metabolomics Analysis - missing value imputation
metabolomics
updated 21 days ago by
obidobi
▴ 30 • written 5.9 years ago by
spacemorrissey
▴ 280
2
votes
3
replies
2.1k
views
Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!!
genome
next-gen
software-error
Assembly
updated 16 hours ago by
Ram
43k • written 4.0 years ago by
memy
▴ 20
5
votes
5
replies
2.1k
views
WGCNA HeatMap correlating modules and sample conditions
RNAseq
heatmap
WGCNA
conditions
clustering
updated 29 days ago by
GenoMax
140k • written 2.1 years ago by
Raito92
▴ 90
0
votes
3
replies
2.0k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 26 days ago by
trkfs
• 0 • written 11 months ago by
mohyeddine.taleb
• 0
0
votes
4
replies
2.0k
views
Ribo-seq rRNA and other contaminants Fasta file for S. pombe
ribo-seq
pombe
fasta
rRNA cleaning
updated 13 days ago by
GenoMax
140k • written 6.7 years ago by
hdmagpantay
• 0
1
vote
3
replies
2.0k
views
psmc bootstrapping help
bootstrap
psmc
updated 3 days ago by
xuby963
• 0 • written 3.1 years ago by
truebeliever24
▴ 50
4
votes
1
reply
2.0k
views
Common reads between two fastq files
exome
sequence
Assembly
updated 14 days ago by
Ram
43k • written 5.2 years ago by
Inquisitive8995
▴ 270
0
votes
1
reply
1.8k
views
Speed up PHASE software for haplotype inference
multithreading
unix
haplotype
updated 6 days ago by
WANG
• 0 • written 8.2 years ago by
kshitijtayal
▴ 40
2
votes
5
replies
1.8k
views
alignement and Variant calling with BWA and samtools
variant-calling
samtools
BWA
updated 2 days ago by
Ram
43k • written 2.9 years ago by
simon.burgermeister
▴ 30
1
vote
1
reply
1.8k
views
Intronic Variant Filtering
variant-calling
snp
updated 2 days ago by
Ram
43k • written 6.7 years ago by
cvu
▴ 180
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
1 day ago by
Zeng Jingyu
▴ 60
0
votes
5
replies
1.7k
views
6 follow
how to know what adapter sequences to trim for RNA-seq?
fastq
RNA-seq
cutadapt
updated 19 days ago by
Brian Bushnell
20k • written 12 months ago by
lunarskye222
• 0
0
votes
4
replies
1.7k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing
illumina
updated 28 days ago by
charbelelias30
• 0 • written 3.3 years ago by
WhiteN8
• 0
1
vote
3
replies
1.7k
views
Normalise batch effects for Percent Spliced In (PSI) matrice
combat
sva
splicing
updated 27 days ago by
Yogi
▴ 70 • written 5.2 years ago by
ZheFrench
▴ 550
3
votes
5
replies
1.7k
views
How to collapse leaves with the same name in ETE3 tree?
python
ete3
updated 13 days ago by
Yogesh
• 0 • written 2.7 years ago by
Andrzej Zielezinski
11k
0
votes
2
replies
1.7k
views
Adding gene symbol to GRanges for calculation purposes
R
updated 8 days ago by
QX
• 0 • written 3.1 years ago by
mm2568
• 0
1
vote
3
replies
1.6k
views
IndexError: list assignment index out of range | Needleman-Wunsch Algorithm - Python
Python
Needleman-Wunsch
Dynamic-Programming
updated 14 days ago by
Ram
43k • written 3.0 years ago by
Anonymous
▴ 10
0
votes
1
reply
1.6k
views
What is the best way to perform a PCA on .vcf of closely related bacteria?
variant-calling
updated 2 days ago by
Ram
43k • written 3.0 years ago by
d.s.account
• 0
2
votes
4
replies
1.6k
views
bowtie2 maximum value of MAPQ
bowtie2
bowtie
updated 3 days ago by
axol0tl
• 0 • written 3.6 years ago by
sami
▴ 30
0
votes
1
reply
1.5k
views
Freebayes - not detecting some ALT alleles
variant-calling
freebayes
vcf
updated 2 days ago by
Ram
43k • written 3.3 years ago by
z.klinovska
• 0
4
votes
4
replies
1.5k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
updated 18 days ago by
cmdcolin
★ 3.7k • written 15 months ago by
Arton
• 0
4
votes
9
replies
1.4k
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
updated 22 days ago by
ATpoint
81k • written 10 months ago by
DanielEB_fisk
▴ 20
3
votes
3
replies
1.4k
views
Simulate 100 Reads from .fastq file | FASTQC
fastq
FASTQC
Linux
updated 14 days ago by
Ram
43k • written 3.0 years ago by
Anonymous
▴ 10
0
votes
8
replies
1.4k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 14 days ago by
xiangbinruan
• 0 • written 18 months ago by
Phoebe Magdy
• 0
0
votes
4
replies
1.4k
views
Building multiple consensus sequences from multiple fasta sequences
next-gen-sequencing
sequence
alignment
updated 18 days ago by
doppelganger1030
• 0 • written 4.7 years ago by
miss
• 0
1
vote
1
reply
1.4k
views
Lowercase variants reported by SomaticSniper
variant-calling
SomaticSniper
updated 2 days ago by
Ram
43k • written 6.7 years ago by
Inés Sentís
▴ 10
0
votes
1
reply
1.4k
views
Dealing with a large sample for variant calling
NGS
alignment
variant-calling
joint-calling
updated 2 days ago by
Ram
43k • written 5.3 years ago by
Mehulsharma.253
▴ 30
832 results • Page
2 of 17
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after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
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The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
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What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
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Ugh. I've definitely done this one before as well. And was none too happy about it.
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fastqc -o output.html input.fastq ctrl+c ctrl+v
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What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
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140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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