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103,113 results • Page
1 of 2063
Sort: Rank
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0
votes
0
replies
5
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Does anyone know any packages that test to make sure ribosomal depletion took place? After illumina tru seq protocol
Ribosomal
sequencing
Contimination
RNA
Packages
10 minutes ago by
kcarery
• 0
0
votes
0
replies
21
views
Tool:
Briefings in Bioinformatics: Hiplot visualization toolkit
mining
data
visualization
bioinformatics
1 hour ago by
Jianfeng
• 0
1
vote
4
replies
125
views
load csv file to edgeR
RNAseq
edgeR
updated 2 hours ago by
Gordon Smyth
★ 4.7k • written 10 hours ago by
Super
• 0
0
votes
1
reply
59
views
Duplicate chromosome location columns in a bed file makes problem in importing them into R
granges
bedtools
r
samtools
bowtie2
updated 3 hours ago by
cmdcolin
★ 2.2k • written 6 hours ago by
minoo
▴ 10
679
votes
160
replies
89k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 11 weeks ago by
Biostar
860 • written 5.6 years ago by
Istvan Albert
93k
0
votes
2
replies
51
views
using txt file to pass pathways for pipelines
muscle
bash
file
seqkit
fasta
28 minutes ago by
Hugo
• 0
0
votes
0
replies
22
views
How to analyze the mirbase mature sequence aligned miRNA output file
mirna
ncbiblast
NGS
mirbase
miRNA
data
analysis
conserved
updated 4 hours ago by
lieven.sterck
14k • written 4 hours ago by
khq5801
• 0
0
votes
0
replies
30
views
Retain non-variable sites after phasing with shapeit4
phasing
vcf
shapeit
awk
shapeit4
4 hours ago by
pabe
▴ 10
3
votes
1
reply
59
views
Forum:
Programming languages in industry
programming
language
updated 1 hour ago by
Medhat
9.3k • written 5 hours ago by
m.monikus
▴ 20
0
votes
0
replies
30
views
Estimating divergence from EPO ancestral sequences in primates
EPO
alignment
divergence
mutation
primate
6 hours ago by
spiral01
▴ 110
0
votes
4
replies
181
views
BWA alignment/Samtools; Fail to read the header
bwa
samtools
updated 4 hours ago by
Pierre Lindenbaum
146k • written 1 day ago by
Qboy
• 0
0
votes
0
replies
42
views
Script or tool to compare more than two .cls files in R or Python
R
Python
updated 30 minutes ago by
cpad0112
21k • written 6 hours ago by
Alex S
• 0
0
votes
1
reply
43
views
export image from cnet plot and bar plot
centplot
updated just now by
cpad0112
21k • written 8 hours ago by
Shakiba
• 0
1
vote
3
replies
103
views
resolving specific clusters from data (spectral clustering)
clustering
updated 9 hours ago by
Mensur Dlakic
★ 20k • written 13 hours ago by
benformatics
★ 2.9k
1
vote
2
replies
107
views
txt file process in linux
linux
awk
updated 9 hours ago by
ohu20a
▴ 10 • written 10 hours ago by
Super
• 0
0
votes
6
replies
139
views
6 follow
Supplementary alignments in BAM-file
reads
Supplementary
galaxy
Samtools
bamfiles
updated 7 hours ago by
cmdcolin
★ 2.2k • written 12 hours ago by
mokbel73
• 0
0
votes
3
replies
84
views
BWA-mem - Different alignment numbers to same reference sequence
BWA-mem
updated 11 hours ago by
GenoMax
117k • written 11 hours ago by
Steven
• 0
0
votes
0
replies
35
views
How to get SNP annotation file for GTEx data
SNP
GTEx
annotation
rsid
12 hours ago by
rheab1230
▴ 50
0
votes
1
reply
114
views
ESTIMATION OF LEVEL OF CYTOKINES FROM BULK RNAseq
rnaseq
r
tcga
bulkrnaseq
updated 4 hours ago by
ATpoint
62k • written 1 day ago by
leticia
▴ 20
1
vote
1
reply
66
views
Minimum and maximum depth filter - vcftools
depth
vcftools
updated 9 hours ago by
Ram
36k • written 12 hours ago by
Matteo
• 0
5
votes
5
replies
143
views
Filtered reads from assembly and raw reads?
sequencing
denovo
assembly
updated 8 hours ago by
GenoMax
117k • written 12 hours ago by
el97004
▴ 50
1
vote
2
replies
121
views
The nightmare of coordinate systems
one-based
zero-based
lef-aligned
right-aligned
updated 14 hours ago by
tomas4482
▴ 170 • written 17 hours ago by
Ana
• 0
4
votes
17
replies
381
views
7 follow
How to split a long protein sequence in small sequences with same header?
fasta
updated 10 hours ago by
cpad0112
21k • written 1 day ago by
FelipeMSD
• 0
0
votes
0
replies
50
views
Convert a List to .loom File in R for scVelo
velocyto.R
Seurat
scVelo
loom
16 hours ago by
630720255
• 0
0
votes
3
replies
86
views
error running fgsea
gene
onthology
fgsea
updated 15 hours ago by
ATpoint
62k • written 16 hours ago by
Chironex
▴ 30
4
votes
4
replies
192
views
Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq objects
time
points
exposure
drug
DEGs
multiple
DESEQ2
updated 16 hours ago by
i.sudbery
14k • written 1 day ago by
salman_96
▴ 60
2
votes
5
replies
157
views
enhanced volcano label point
rnaseq
enhancedvolcano
updated 11 hours ago by
cpad0112
21k • written 17 hours ago by
edus_bioinfo
▴ 20
1
vote
4
replies
116
views
GATK CombineGVCFs with genotypes './.'
GATK
CombineGVCFs
16 hours ago by
ttom
▴ 220
0
votes
0
replies
58
views
CNV annotation using GAIA
cnv
gaia
11 hours ago by
melissachua90
▴ 40
1
vote
1
reply
93
views
What is the difference between fastq.gz and fastq.gz.len
dataset
fastq
sequencing
updated 17 hours ago by
cpad0112
21k • written 18 hours ago by
MobiusT
• 0
0
votes
0
replies
56
views
News:
Automate your NGS data analyses and create reproducible/scalable pipelines with NextFlow
pipeline
Nextflow
automation
19 hours ago by
David Langenberger
9.7k
4
votes
10
replies
4.3k
views
Running multiQC on more than one file Log.final.out from STAR
multiqc
star
updated 20 hours ago by
Tz
• 0 • written 5.7 years ago by
cristian
▴ 310
0
votes
1
reply
76
views
Metabolic network construction and modelling
Modelling
proteomics
Metabolomics
Metabolic
expression
network
Gene
updated 18 hours ago by
andres.firrincieli
★ 2.5k • written 20 hours ago by
cdjeu
▴ 10
0
votes
2
replies
122
views
why the syntax error comes when i use the same command in loop in bash linux
awk
updated 20 hours ago by
Michael Dondrup
52k • written 21 hours ago by
Priya
▴ 20
1
vote
5
replies
222
views
What would the items look like if we put them on a length scale?
length-scale
scale
time-scale
biological-process
offtopic
updated 9 hours ago by
Mensur Dlakic
★ 20k • written 1 day ago by
user366312
▴ 10
0
votes
3
replies
149
views
Changing output directory for bamtools split
bamtools
sge
updated 16 hours ago by
GenoMax
117k • written 1 day ago by
phosphorus
▴ 10
0
votes
0
replies
119
views
ZINC Drug like pdbqt format file that the number I download doesn't match the number display in web site
autodock
ZINC
Drug
like
1 day ago by
华北
• 0
0
votes
2
replies
137
views
Getting sequence information by using atoms
atoms
python
cif
protein
updated 17 hours ago by
cpad0112
21k • written 1 day ago by
drbioengineer
• 0
0
votes
3
replies
147
views
0% adapter bases after demultiplexing 10x data and "undetermined" sample
10x
BCLconvert
illumina
snrnaseq
updated 16 hours ago by
GenoMax
117k • written 1 day ago by
demoraesdiogo2017
▴ 60
11
votes
8
replies
6.2k
views
8 follow
.mcool to .hic
RNA-Seq
updated 1 day ago by
zsq.phy
▴ 10 • written 3.4 years ago by
dimitrischat
▴ 180
0
votes
6
replies
154
views
How to deal with conflicting INFO field names in SnpSift?
SnpSift
snpEff
1 day ago by
bdolin
▴ 90
7
votes
16
replies
361
views
The STAR program does not work after the mapping
STAR
updated 10 hours ago by
GenoMax
117k • written 1 day ago by
pavelasquezv
▴ 20
0
votes
0
replies
108
views
Job:
Bioinformatics Pipeline Developer - NatureMetrics (Guildford, Surrey)
jobs
recruitment
1 day ago by
Daniel
• 0
3
votes
1
reply
152
views
Low exonic mapping of RNASeq data to draft genome. Should I suspect poor annotation?
rnaseq
mapping
updated 1 day ago by
GenoMax
117k • written 1 day ago by
CephBirk
▴ 20
1
vote
3
replies
130
views
How to subset a GVCF using GATK SelectVariants
GATK
SelectVariants
1 day ago by
ttom
▴ 220
3
votes
6
replies
322
views
Convert a BAM from GRCh37 to hg19?
hg19
SAM
GRCh37
BAM
h37
updated 1 day ago by
Giovanni M Dall'Olio
27k • written 4 days ago by
Joel Wallenius
▴ 100
0
votes
1
reply
115
views
gene library composition
composition
rna-seq
updated 1 day ago by
Rafael Soler
▴ 430 • written 1 day ago by
edus_bioinfo
▴ 20
4
votes
2
replies
197
views
Extract all regions in a genome that are not assembly gaps from a FASTA file quickly
fasta
1 day ago by
Ivan
▴ 50
0
votes
1
reply
418
views
News:
Hands-On RNA-Seq Data Analysis Workshop in Leipzig, Germany (October 25-28, 2022)
RNA-Seq
Transcriptomics
NGS
Workshop
1 day ago by
David Langenberger
9.7k
0
votes
0
replies
81
views
In silico pcr for Unite database
mothur
Unite
18 hours ago by
kiko.114
• 0
103,113 results • Page
1 of 2063
Recent Votes
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Programming languages in industry
Programming languages in industry
C: Why is 0/0 homozygous reference call in VCF useful information?
Comment: load csv file to edgeR
TLEN field in SAM format
Answer: Filtered reads from assembly and raw reads?
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Comment: using txt file to pass pathways for pipelines
by
Hugo
• 0
Thanks for the help Pierre, but it did not work. I receive the same message for every iteration (just change the file pathway): ' errno=…
Comment: export image from cnet plot and bar plot
by
cpad0112
21k
It's working fine for me.
Answer: Programming languages in industry
by
Medhat
9.3k
- Python (Data analysis and machine learning) - Pipeline building Snakemake or Nextflow (most industry lean to work with Nextflow) - Compil…
Comment: load csv file to edgeR
by
Gordon Smyth
★ 4.7k
I think you're reading `?goana.DGELRT` rather than `?goana`. Type `methods(goana)` to see the methods available. The default method support…
Answer: load csv file to edgeR
by
Gordon Smyth
★ 4.7k
I assume that the differential results table is complete and contains all expressed genes rather than just the 12 genes shown in your post.…
Answer: Duplicate chromosome location columns in a bed file makes problem in importing t
by
cmdcolin
★ 2.2k
your bed file is actually a BEDPE file because you specified to use the -bedpe flag to `bedtools bamtobed`. it has two chr, start, and end …
Comment: Running multiQC on more than one file Log.final.out from STAR
by
ATpoint
62k
Did you test that? It still searches `.` so the entire `$(pwd)`, no?
Comment: load csv file to edgeR
by
ATpoint
62k
`?goana` indicates that the function needs `an DGELRT or DGEExact object`, so that you cannot easily rebuild (if at all) from that table. S…
Comment: using txt file to pass pathways for pipelines
by
Pierre Lindenbaum
146k
cat name_path3.txt | paste - - | while read entrada saida ; do muscle -in "${entrada}" -out "${saida}" ; done
Comment: BWA alignment/Samtools; Fail to read the header
by
Qboy
• 0
It is the name of the fastq.gz file. It is not part of the file. My apologies. it just pops up when I run the bash script in prompt. This…
Comment: BWA alignment/Samtools; Fail to read the header
by
Pierre Lindenbaum
146k
what i sthat altai5 in front of '@SQ' ?
Comment: BWA alignment/Samtools; Fail to read the header
by
Qboy
• 0
Dear Pierre, Here is the answer to your questions (Iguess it works): altai5@SQ SN:NC_036879.1 LN:224244399 @SQ SN:NC_…
Comment: Supplementary alignments in BAM-file
by
cmdcolin
★ 2.2k
for what it's worth, "supplementary alignments" can be quite interesting. they often indicate things like SVs
Comment: Filtered reads from assembly and raw reads?
by
GenoMax
117k
In that case use an aligner of your choice and extract reads that map: https://www.biostars.org/p/56246/#56251 Be sure to get primary alig…
Comment: Filtered reads from assembly and raw reads?
by
el97004
▴ 50
Yeah I was just trying to find the set of reads that were used to make up the final assembly. Some of those raw reads will definitely not a…
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