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1,000 results • Page
2 of 20
Sort: replies
Rank
Views
Votes
Replies
2
votes
12
replies
4.4k
views
Adding barcodes to forward and reverse reads after sequencing
obitools
barcoding
next-gen-sequencing
updated 10 months ago by
Ram
41k • written 8.6 years ago by
cmogren
▴ 20
1
vote
12
replies
4.1k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq
alignment
sequencing
updated 11 months ago by
ATpoint
78k • written 6.2 years ago by
SMILE
▴ 170
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
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
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
12 months ago by
langziv
▴ 50
2
votes
12
replies
1.3k
views
gatk Funcotator
vcf
Funcotator
gatk
5 months ago by
Saurabh
• 0
6
votes
12
replies
1.3k
views
Help with error in cellranger
Cellranger
updated 6 months ago by
GenoMax
136k • written 6 months ago by
Chris
▴ 230
7
votes
12
replies
1.4k
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA
integrated
ATAC-seq
updated 6 months ago by
Sasha
▴ 770 • written 6 months ago by
Chris
▴ 230
0
votes
12
replies
937
views
scrna seq analysis - doublets
scrna
seq
code
r
updated 5 months ago by
Nitin Narwade
★ 1.5k • written 5 months ago by
bioinformatics
▴ 20
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
2
votes
12
replies
2.8k
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
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
5
votes
12
replies
1.0k
views
Data from an experiment
single-cell
updated 9 months ago by
GenoMax
136k • written 9 months ago by
Chris
▴ 230
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
7
votes
12
replies
1.5k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome
bwa
bash
updated 4 weeks ago by
Ram
41k • written 3.8 years ago by
Karma
▴ 310
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
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
732
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
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
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
5
votes
11
replies
927
views
Interpret IGV output inversion
variant-calling
IGV
alignment
updated 3 months ago by
cmdcolin
★ 3.4k • written 3 months ago by
pablo
▴ 300
1
vote
11
replies
3.5k
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
1.1k
views
Check Strandedness
Check_Strandedness
how_are_we_stranded_here
leafcutter
bash
updated 6 weeks ago by
Brian Bushnell
20k • written 3 months ago by
Y
• 0
1
vote
11
replies
937
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly
Trinity
RNA-seq-analysis
updated 10 weeks ago by
GenoMax
136k • written 3 months ago by
langziv
▴ 50
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
11
replies
683
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
4 days ago by
sil_bioinfo
▴ 40
6
votes
11
replies
1.4k
views
Calculate RPKM
RPKM
8 months ago by
Chris
▴ 230
0
votes
11
replies
1.3k
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
3.1k
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
945
views
Normalization for microarrays >1000+ samples?
microarray
normalization
oligo
10 weeks ago by
evmae
• 0
2
votes
10
replies
2.9k
views
6 follow
Split plink files by a number of SNPs
GWAS
SNP
plink
updated 9 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
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
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
950
views
Coverage histogram query
Alignment
3 months ago by
prasundutta87
▴ 660
1
vote
10
replies
5.6k
views
which field has more scope Bioinformatics or Biomedical engineering at MS level???
biomedical
updated 8 months ago by
Ram
41k • written 7.3 years ago by
purpledora100
• 0
5
votes
10
replies
942
views
the distribution of log2Fc and t value are not similar for bulk RNA-seq
decoupleR
RNA-seq
3 months ago by
alwayshope
▴ 40
4
votes
10
replies
3.9k
views
TCGA normalized count data of 1000 samples for DGE
RNA-Seq
TCGA
updated 10 months ago by
Ram
41k • written 8.6 years ago by
David_emir
▴ 470
3
votes
10
replies
823
views
STAR index not working
STAR
RNA-Seq
10 weeks ago by
camillab.
▴ 150
1
vote
10
replies
916
views
Do monoclonal antibodies have a blocking effect?
block
antibody
offtopic
updated 3 months ago by
Jeremy
▴ 860 • written 3 months ago by
jinyu
▴ 10
1
vote
10
replies
1.2k
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 10 weeks ago by
jeffhsu3
• 0 • written 5 months ago by
fra.silvestro
▴ 10
8
votes
10
replies
1.7k
views
PyWGCNA
WGCNA
5 months ago by
yoshifumimiya
▴ 40
3
votes
10
replies
1.7k
views
Error with FindConservedMarkers()
FindConservedMarkers
9 months ago by
Chris
▴ 230
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
5
votes
10
replies
694
views
Error when viewing a bam file
samtools
updated 5 months ago by
Ram
41k • written 7 months ago by
Chris
▴ 230
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
2
votes
10
replies
7.1k
views
fq.gz file use
BioEdit
R
updated 8 months ago by
Ram
41k • written 4.8 years ago by
choi.yisoo.hi
• 0
4
votes
10
replies
716
views
Extract unmapped reads OR reads covering chromosome 6 from a bam file?
fastq
bam
samtools
picard
9 months ago by
dps2501
▴ 20
1,000 results • Page
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Answer: Help with gatk CreateSequenceDictionary
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Are we tricking ourselves with batch effect correction?
Answer: Are we tricking ourselves with batch effect correction?
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Comment: Microbial gene coverage from blast result
by
aanchal.yadav
• 0
What is qcovhsp (high scoring segment pair) in BLAST output. Can we use this parameter to calculate the gene coverage?
Answer: Best way to normalize transcript reads data for PCA & correlation and further bi
by
Jeremy
▴ 860
Scaling the data will give you Z-scores. This is a standard way of preparing data for PCA. I would also suggest trying a center-log-ratio…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
peanut
• 0
Thank you for your answer,but after verifying the protein file, it seems there is no problem. Even if there are missing codons, the program…
Comment: Help with gatk CreateSequenceDictionary
by
Chris
▴ 230
It worked! Thanks Matt!
Comment: Finding human .vcf files online to download
by
cmdcolin
★ 3.4k
i can't really tell you why your code doesn't work if you dont provide it. and, if you describe as much as possible what your goals are, th…
Answer: Help with gatk CreateSequenceDictionary
by
MatthewP
★ 1.3k
maybe try?: -R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg3…
Comment: Java error while running HiCDC overview code
by
Brian Bushnell
20k
Looks like you have corrupt or improperly-formatted input. It's expecting to parse a floating-point number where the word "score" appears.…
Comment: what should I do if I get a compromised sample of scRNA-seq data?
by
dsull
★ 5.1k
The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a Q…
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by
enriquesan
• 0
...........
Comment: FastQC without yellow box
by
lobelino
• 0
Thank you for your answer.
Comment: FastQC without yellow box
by
lobelino
• 0
My question is Can I trust the statistics of my data I didn't get any yellow boxes, but I got high media values. Why I didn't get any yello…
Answer: FastQC without yellow box
by
ATpoint
78k
The box is the quartiles, the red line the median. Please google how to read a box plot. Your data is good in terms of base quality.
Comment: FastQC without yellow box
by
Ram
41k
What's your question?<a href="" title="Text added because biostars parser needs it"></a>
Comment: vcftools
by
Ram
41k
Deprecated tools don't just stop producing output/errors, that's now how deprecation works.
Comment: vcftools
by
Ram
41k
> couldn't get any output What does that mean? What did you see on the screen when you ran this command? Did the command run successfully …
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