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1,000 results • Page
2 of 20
Sort: replies
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Votes
Replies
2
votes
12
replies
2.7k
views
how to get to a VCF from bam files
Mpileup
Samtools
BAM
bcftools
VCF
updated 8 months ago by
Ram
41k • written 8 months ago by
Human
• 0
6
votes
12
replies
1.4k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 8 months ago by
Ram
41k • written 4.8 years ago by
english.server
▴ 290
2
votes
12
replies
1.3k
views
gatk Funcotator
vcf
Funcotator
gatk
5 months ago by
Saurabh
• 0
6
votes
12
replies
1.2k
views
Help with error in cellranger
Cellranger
updated 6 months ago by
GenoMax
136k • written 6 months ago by
Chris
▴ 230
6
votes
12
replies
1.5k
views
VCF files 101 - for people from non Bioinformatics Background
vcf
sequencing
genome
variant-calling
updated 8 months ago by
Ram
41k • written 3.3 years ago by
akshaykum684
▴ 20
8
votes
12
replies
3.4k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 8 months ago by
Ram
41k • written 2.3 years ago by
daver.v
▴ 30
1
vote
12
replies
1.4k
views
Volcano plot interpretation
EnhancedVolcano
volcano-plot
updated 9 months ago by
Ram
41k • written 2.4 years ago by
fahim
▴ 20
0
votes
12
replies
807
views
Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cell Ranger.
fixed-RNA-profiling
chromium
cellranger
scFFPE
updated 5 weeks ago by
GenoMax
136k • written 5 weeks ago by
bk11
★ 1.8k
0
votes
12
replies
1.9k
views
bedtools intersect issue
bed
bedtools
updated 8 months ago by
Ram
41k • written 5.3 years ago by
elisheva
▴ 120
5
votes
12
replies
991
views
Data from an experiment
single-cell
updated 9 months ago by
GenoMax
136k • written 9 months ago by
Chris
▴ 230
3
votes
12
replies
2.6k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 6 months ago by
Pegasus
▴ 90 • written 4.1 years ago by
mnazir
▴ 10
2
votes
12
replies
4.4k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 9 months ago by
Ram
41k • written 8.6 years ago by
cmogren
▴ 20
4
votes
12
replies
1.5k
views
Bulk RNA seq: all p adjusted are the same
p-adj
RNA-seq
differential-gene-expression
updated 11 months ago by
Ram
41k • written 18 months ago by
nils.simon.biology
▴ 10
7
votes
12
replies
1.4k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome
bwa
bash
updated 27 days ago by
Ram
41k • written 3.8 years ago by
Karma
▴ 310
0
votes
12
replies
2.9k
views
Allpaths- Keep getting ConvertToFastbQualb.pl failed for group 'paired_ends' when I run PrepareAllPaths
next-gen
Assembly
updated 11 months ago by
Ram
41k • written 8.4 years ago by
mafireyi
▴ 80
1
vote
12
replies
4.1k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 10 months ago by
ATpoint
78k • written 6.2 years ago by
SMILE
▴ 170
7
votes
12
replies
1.3k
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 6 months ago by
Sasha
▴ 760 • written 6 months ago by
Chris
▴ 230
0
votes
12
replies
921
views
scrna seq analysis - doublets
scrna
seq
code
r
updated 4 months ago by
Nitin Narwade
★ 1.5k • written 4 months ago by
bioinformatics
▴ 20
0
votes
12
replies
3.1k
views
comparative analysis of two strains of bacteria's genomes
genome
gene
updated 6 months ago by
Ram
41k • written 6.1 years ago by
fonteneaudam
▴ 20
0
votes
12
replies
1.4k
views
Splitting CRAM files
CRAM-files
sequence-alignment
11 months ago by
langziv
▴ 50
6
votes
11
replies
1.4k
views
Calculate RPKM
RPKM
8 months ago by
Chris
▴ 230
0
votes
11
replies
1.5k
views
count file having zero
RNA-Seq
next-gen
alignment
updated 5 months ago by
Ram
41k • written 4.8 years ago by
BioBaby
▴ 20
1
vote
11
replies
3.4k
views
bedtools fisher interpretation of "in -a" "not in -b"
fisher
bedtools
intersection
updated 9 months ago by
Ram
41k • written 5.8 years ago by
jomo018
▴ 720
4
votes
11
replies
1.2k
views
PCA WITH PLINK
PLINK
updated 3 months ago by
Kevin Blighe
86k • written 3 months ago by
adriana michelle
• 0
5
votes
11
replies
3.4k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 8 months ago by
Ram
41k • written 5.6 years ago by
HG
▴ 30
2
votes
11
replies
645
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
12 days ago by
sil_bioinfo
▴ 30
4
votes
11
replies
1.0k
views
Check Strandedness
Check_Strandedness
how_are_we_stranded_here
leafcutter
bash
updated 6 weeks ago by
Brian Bushnell
19k • written 3 months ago by
Y
• 0
5
votes
11
replies
907
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 3 months ago by
cmdcolin
★ 3.4k • written 3 months ago by
pablo
▴ 300
5
votes
11
replies
724
views
Make heatmap for RNA-seq with non replicate
RNA-seq
updated 3 months ago by
Ram
41k • written 3 months ago by
Chris
▴ 230
1
vote
11
replies
922
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 9 weeks ago by
GenoMax
136k • written 3 months ago by
langziv
▴ 50
0
votes
11
replies
1.2k
views
Problem with Trimmomatic Multiple Paired-End sequencing.
Trimmomatic
updated 10 months ago by
GenoMax
136k • written 10 months ago by
john
• 0
4
votes
11
replies
3.0k
views
Please add an explicit type tag :NAME
software-error
next-gen
genome
updated 10 months ago by
Ram
41k • written 5.6 years ago by
mahdikhadem95
▴ 30
0
votes
11
replies
935
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
10 weeks ago by
evmae
• 0
0
votes
11
replies
2.0k
views
i want to convert .ht2 files into FASTA file
GATK
HISAT2
FASTA
updated 5 months ago by
Ram
41k • written 4.5 years ago by
saumya.sharma1509
• 0
2
votes
10
replies
7.0k
views
fq.gz file use
BioEdit
R
updated 8 months ago by
Ram
41k • written 4.7 years ago by
choi.yisoo.hi
• 0
0
votes
10
replies
7.4k
views
Error: reads file does not look like a fastq file
fastq
bowtie2
ChIP-Seq
updated 8 months ago by
Ram
41k • written 7.2 years ago by
addilynn.beach
▴ 40
1
vote
10
replies
5.6k
views
which field has more scope Bioinformatics or Biomedical engineering at MS level???
biomedical
updated 7 months ago by
Ram
41k • written 7.3 years ago by
purpledora100
• 0
3
votes
10
replies
806
views
STAR index not working
STAR
RNA-Seq
9 weeks ago by
camillab.
▴ 150
5
votes
10
replies
938
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
3 months ago by
alwayshope
▴ 40
2
votes
10
replies
2.9k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 8 weeks ago by
Raygozak
★ 1.4k • written 5.4 years ago by
kakukeshi
▴ 80
2
votes
10
replies
4.1k
views
Error encountered while running stattest from ballgown package
bioconductor
RNA-Seq
ballgown
stattest
updated 7 months ago by
Ram
41k • written 6.6 years ago by
lakhujanivijay
5.8k
7
votes
10
replies
1.6k
views
Ubuntu 20.04 Crash
Ubuntu
updated 9 months ago by
Ram
41k • written 22 months ago by
bala
• 0
3
votes
10
replies
1.6k
views
Error with FindConservedMarkers()
FindConservedMarkers
9 months ago by
Chris
▴ 230
4
votes
10
replies
709
views
Extract unmapped reads OR reads covering chromosome 6 from a bam file?
fastq
bam
samtools
picard
9 months ago by
dps2501
▴ 20
1
vote
10
replies
2.2k
views
Weird results for scRNA-seq
scRNA-seq
GEO
updated 11 months ago by
Giuseppe
▴ 70 • written 11 months ago by
tujuchuanli
▴ 100
1
vote
10
replies
613
views
file conversion from gtf to gff3 for evidence modeler
gff3
stringtie
gtf
5 weeks ago by
rj.rezwan
• 0
2
votes
10
replies
1.4k
views
multiple FASTA sequnces in to one full sequnce according to their chromosome number
NGS
FASTA
bam
updated 8 months ago by
Ram
41k • written 4.7 years ago by
Anu
• 0
1
vote
10
replies
902
views
Do monoclonal antibodies have a blocking effect?
block
antibody
offtopic
updated 3 months ago by
Jeremy
▴ 840 • written 3 months ago by
jinyu
▴ 10
1
vote
10
replies
2.9k
views
How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment
BLAST
tBLASTn
updated 6 months ago by
Ram
41k • written 4.7 years ago by
Kumar
▴ 120
7
votes
10
replies
1.5k
views
col as names [solved]
R
updated 8 months ago by
Ram
41k • written 4.7 years ago by
demoraesdiogo2017
▴ 100
1,000 results • Page
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Recent Votes
How to make a survival plot for a gene between High expression and low expression samples?
Comment: bwa mem hangs after a few thousand reads
bwa mem hangs after a few thousand reads
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
Answer: Generate Read counts from bam file
Comment: Generate Read counts from bam file
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Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 170
Use option `-v` with value of 4 or above to help diagnose the issue: `-v INT` Control the verbose level of the output. This option has not…
Comment: bwa mem hangs after a few thousand reads
by
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▴ 170
Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
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Thank you, I really appreciate your insight! I will look into the dropouts I have.
Answer: Generate Read counts from bam file
by
NextGenSeek
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Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
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136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
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18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
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Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
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by
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its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
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Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
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Trying to bump this
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The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
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78k
Please provide data as dput(), not via any random dropbox, that could be anything (also malware, theoretically). If log transformation crea…
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Hi Pierre, so does samjdk support single-end reads for extracting chimeric reads? I've aligned my virus to the human reference, sorted the …
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
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dthorbur
▴ 870
You can try `scale_y_sqrt()` instead if you don't like the look of the log10 transformation. As an aside, it doesn't look like your fill va…
Comment: Making multiple box plots with relative abundance in R
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ohtang7
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Thank you!! I really appreciate your help.
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