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1,000 results • Page
1 of 20
Sort: replies
Rank
Views
Votes
Replies
16
votes
38
replies
15k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 9 months ago by
Ram
37k • written 8.0 years ago by
Mo
▴ 920
23
votes
22
replies
36k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 9 weeks ago by
Nicole
• 0 • written 4.7 years ago by
gaelgarcia
▴ 250
5
votes
22
replies
6.3k
views
SVM for classified gene expression data
R
svm
microarray
updated 6 months ago by
Ram
37k • written 7.1 years ago by
Shaurya Jauhari
▴ 50
2
votes
22
replies
1.0k
views
6 follow
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
pedigree
linkage
genetics
3 months ago by
Joel Wallenius
▴ 100
0
votes
21
replies
1.4k
views
HTSeq-Count: no_feature too high?
htseq-count
3 months ago by
sea.joson
▴ 10
5
votes
20
replies
3.1k
views
DiscoSnp Segmentation fault
snp
discosnp
updated 4 months ago by
Ram
37k • written 7.4 years ago by
Hans
▴ 130
8
votes
20
replies
1.7k
views
Converting runpsipred Script to Work on Windows OS
psipred
windows
updated 8 months ago by
Ram
37k • written 4.5 years ago by
Bara'a
▴ 270
18
votes
19
replies
1.5k
views
6 follow
Extremely important marker gene has many reads based on IGV viewer but no quantified reads
rna-seq
sequencing
igv
alignment
next-gen
updated 9 weeks ago by
Ram
37k • written 4.1 years ago by
rbkh09
• 0
0
votes
19
replies
963
views
scatterplot in R
microarray
expression
gene
updated 4 months ago by
Ram
37k • written 4 months ago by
bioinformatics
▴ 10
7
votes
19
replies
2.3k
views
mapping script process sleeping on server.
alignment
updated 8 months ago by
Ram
37k • written 7.9 years ago by
lvogel
▴ 30
2
votes
18
replies
1.6k
views
I need help in this
gene
weblems
alignment
updated 6 months ago by
Ram
37k • written 7.1 years ago by
efosa15
• 0
3
votes
18
replies
785
views
6 follow
What sequencing/alignment artifact is this?
variants
mutect
sequencing
alignment
mitochondria
3 months ago by
lacb
▴ 30
7
votes
18
replies
7.5k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 11 months ago by
Ram
37k • written 8.2 years ago by
hana
▴ 190
4
votes
18
replies
3.2k
views
Significance of reads mapping to Viruses - FusionCatcher
RNA-Seq
virus
reads
fusion
updated 5 months ago by
Ram
37k • written 7.2 years ago by
Joel TM
▴ 60
0
votes
17
replies
5.4k
views
7 follow
EXITING: because of fatal INPUT file error: could not open read file
mapping
genome
fastq
STAR
updated 11 months ago by
todd.ugine
• 0 • written 2.1 years ago by
merfer0206
• 0
0
votes
17
replies
4.0k
views
Finding True SNPs after hard filtering on GATK
SNP
updated 4 months ago by
Ram
37k • written 7.4 years ago by
jigarnt
▴ 30
0
votes
16
replies
3.5k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 7 months ago by
Ram
37k • written 7.8 years ago by
bharata1803
▴ 550
0
votes
16
replies
1.2k
views
How to convert ncbi gff file to ensembl gff format
file
gff
5 months ago by
yoser4
▴ 10
4
votes
16
replies
926
views
How to extract intron counts from total RNA Sequencing?
featurecounts
RNAseq
htseq
STAR
11 weeks ago by
barrypraveen
▴ 100
19
votes
15
replies
25k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 6 months ago by
Ram
37k • written 7.1 years ago by
dam4l
▴ 180
3
votes
15
replies
1.1k
views
Overlapping regions in a BED file
regions
BED
Sequence
exons
annotation
7 months ago by
Matej
• 0
6
votes
15
replies
891
views
The Best Cloud Solution For Genomics
cloud
data-sharing
genomics
workflow
updated 6 months ago by
Ram
37k • written 7 months ago by
davidmaimoun
▴ 50
0
votes
15
replies
1.3k
views
Chromosome accession numbers correspond to which chromosome?
bam
chromosome
bed
3 months ago by
amy__
▴ 50
7
votes
15
replies
4.4k
views
6 follow
blastn error - NCBI C++ Exception
assembly
blast
alignment
updated 10 months ago by
lieven.sterck
14k • written 22 months ago by
sunnykevin97
▴ 970
0
votes
15
replies
2.9k
views
Identify genes in a tophat aligned bam/sam file
blast
alignment
rna-seq
gene
updated 5 weeks ago by
Ram
37k • written 7.6 years ago by
gchaves
• 0
0
votes
14
replies
972
views
Corrplot heatmap crunched up and unreadable
Corrplot
heatmap
8 months ago by
aropri
▴ 110
2
votes
14
replies
682
views
Annotating the multi sample vcf file
vcf
annotation
7 weeks ago by
Peerzada
• 0
5
votes
14
replies
1.3k
views
Removing sequences that contain deletion mutations in them from a fasta file (with python)
python
6 months ago by
Mustafa
▴ 10
5
votes
14
replies
639
views
How to Calulate Allele Frequency from a VCF File?
frequency
allele
VCF
updated 2 days ago by
Jeremy Leipzig
21k • written 6 days ago by
Emoji
• 0
5
votes
14
replies
1.2k
views
Fastqc genome reads
genome
fastqc
updated 11 months ago by
ATpoint
68k • written 11 months ago by
Ak
▴ 60
0
votes
14
replies
836
views
Error using HTSEq_count
HTSeq
python
18 days ago by
felipead66
▴ 110
1
vote
14
replies
1.4k
views
Counts all read zero after alignment?
alignment
rna-seq
updated 7 months ago by
Ram
37k • written 17 months ago by
tul66893
• 0
6
votes
14
replies
2.5k
views
mapping RNAseq reads to a genbank isoforme that is not in Reference Annotation
RNA-Seq
sequence
cufflinks
new isoform in rnaseq
updated 6 months ago by
Ram
37k • written 7.0 years ago by
fta.mirzadeh
• 0
0
votes
14
replies
3.1k
views
ABySS - Out of memory using 64 cores (520GB)
abyss
assembly
updated 3 months ago by
Ram
37k • written 7.5 years ago by
wjar6718
• 0
9
votes
14
replies
3.6k
views
Explanation on Paired end single index for RNA seq
RNA-Seq
updated 10 months ago by
Ram
37k • written 8.0 years ago by
hothriananya
▴ 70
5
votes
13
replies
5.9k
views
makeblastdb problem for bacterial genomes
blast
makeblastdb
updated 12 months ago by
Ram
37k • written 8.2 years ago by
niu2rseq
▴ 90
2
votes
13
replies
912
views
How to compare differential expression of same genes between two groups?
expression
differential
updated 10 months ago by
swbarnes2
13k • written 10 months ago by
mark.pekarsky
▴ 20
1
vote
13
replies
289
views
RNAseq for DE purpose
RNAseq
updated 15 hours ago by
swbarnes2
13k • written 18 hours ago by
m.habib
• 0
1
vote
13
replies
2.3k
views
If GI number in list1 is present in genbank file, make new list and append location information
python
genbank
biopython
updated 9 months ago by
Ram
37k • written 7.9 years ago by
pawlowac
▴ 80
6
votes
13
replies
5.9k
views
DESeq2 and edgeR - no agreement between results
RNA-Seq
edgeR
DESeq2
updated 5 months ago by
Ram
37k • written 7.2 years ago by
ilyco
▴ 60
2
votes
13
replies
1.2k
views
[RNAseq, featureCounts] Can paired-end data be processed as single end?
paired-end
RNAseq
featureCounts
6 months ago by
Texx
• 0
1
vote
13
replies
810
views
Samtools indexing problem during bwa mem alignment
Alignment
bwa
samtools
7 months ago by
GlouGlou
• 0
1
vote
13
replies
3.2k
views
Clarification on the “orientation” of chromosomal rearrangements in mate-pair or paired-end sequencing
sequencing
alignment
Assembly
updated 9 months ago by
Ram
37k • written 8.0 years ago by
alec_djinn
▴ 380
7
votes
13
replies
3.6k
views
DESeq2: can I correct for relatedness when using data from multiplex families?
DESeq2
RNA-Seq
Multiplex-families
updated 9 months ago by
Ram
37k • written 8.0 years ago by
alesssia
▴ 580
1
vote
13
replies
888
views
Ete3 build - ValueError: Error parsing Phyml result
ete3
ete3toolkit
ete
phyml
build
updated 3 months ago by
Matthias Zepper
2.9k • written 3 months ago by
nitinra
▴ 50
4
votes
13
replies
23k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 7 months ago by
Qboy
• 0 • written 4.9 years ago by
sambioinfo2018
▴ 20
1
vote
13
replies
2.5k
views
Pooled / polyploid samples
discosnp
updated 4 months ago by
Ram
37k • written 7.4 years ago by
tkitapci
▴ 60
12
votes
13
replies
2.1k
views
Gene Expression and Systems Biology (homework)
gene
homework
updated 8 weeks ago by
Ram
37k • written 7.6 years ago by
sarathkurichiyil
• 0
1
vote
12
replies
3.3k
views
why different outputs with applying various extracting fasta sequences tool, which one correct!?
alignment
sequencing
RNA-Seq
updated 3 months ago by
Ram
37k • written 7.5 years ago by
seta
★ 1.7k
0
votes
12
replies
3.5k
views
Problem: kmergenie has a minimum number of input of reads?
K-mers
Kmergenie
updated 9 months ago by
Ram
37k • written 7.9 years ago by
Leandro de Mattos
▴ 90
1,000 results • Page
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Answer: High downstream gene expression
Answer: High downstream gene expression
Answer: High downstream gene expression
Answer: 'SyntaxError': 'return' outside function?
Comment: Analyzing bulk RNA-seq
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Comment: STAR is running but .sam file size does not increase after hours mapping
by
GenoMax
125k
Memory =/= disk storage. Likely you will need to diagnose this yourself since we don't have access to your data/server. Your command obvio…
Comment: STAR is running but .sam file size does not increase after hours mapping
by
luzglongoria
▴ 40
Thanks for your reply. It is not a problem of memory since I can run other mapping analyses with no problem (I get big Sam output files w…
Comment: Translating gene names to entrez id's
by
GenoMax
125k
https://www.biostars.org/u/123097/ : Please post this as a new question. It is not directly related to this thread. Once you do that you ca…
Comment: Translating gene names to entrez id's
by
eliska.ochodkova
• 0
Dear all, I want to use the GoSim package to calculate the IC similarity. I'm trying to set the parameters of setEvidenceLevel(), but wr…
Comment: STAR is running but .sam file size does not increase after hours mapping
by
GenoMax
125k
Is this a server administered by a sys admin? Do you know if individual user accounts have "quota"? If your user account has a storage qu…
Comment: STAR is running but .sam file size does not increase after hours mapping
by
luzglongoria
▴ 40
If I do df -h then I get Filesystem Size Used Avail Use% Mounted on devtmpfs …
Comment: RNASeq differential expression masked by pathways disregulation
by
i.sudbery
16k
It you really do have a reason to suspect that the biology of samples from CC1 is different from the biology of samples from CC2, and that …
Answer: High downstream gene expression
by
i.sudbery
16k
You don't show which species this is. I've taken a quick look at the human and mouse genome at those locations and neither have any genes a…
Comment: Annotating ENS codes to gene name
by
GenoMax
125k
This is a FAQ, Some past threads linked here: https://www.biostars.org/p/9552097/#9552101
Comment: STAR is running but .sam file size does not increase after hours mapping
by
GenoMax
125k
You are not running out of storage quota on the particular disk?
Comment: STAR is running but .sam file size does not increase after hours mapping
by
luzglongoria
▴ 40
I have tried reducing the number of threads but it is the same.
Answer: High downstream gene expression
by
Matthias Zepper
2.9k
1. Impossible to tell from the information you are showing. Could be misalignments, [read-through transcription][1] ([detection pipeline][…
Answer: Annotating ENS codes to gene name
by
Apex92
▴ 240
You can either use biomart to download all gene ids and gene names and then intersect them with your current table. Or you can use your ann…
Comment: CoveragePlot in Signac from MACS2 Object
by
bioinformatics.girl
• 0
This does not work. I called for the gene "Cd8a" for instance for the mouse genome and it says "Gene not found" even though it should appea…
Comment: How to extract the list of genes from TCGA CNV data
by
Kevin Blighe
84k
Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…
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