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1,000 results • Page 4 of 20
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0
votes
16
replies
4.3k
views
Count read with summarizeOverlaps result 0 for all sample
RNA-Seq
updated 22 months ago by 43k • written 9.0 years ago by ▴ 560
3
votes
16
replies
1.5k
views
Problem, getting information only from the last row and not from all the rows
perl
6.0 years ago by ArusjakGevorgyan ▴ 30
1
vote
16
replies
2.7k
views
Merging fastq files from two experiments
FASTQ NGS
updated 5.2 years ago by 20 • written 5.3 years ago by ★ 4.3k
3
votes
16
replies
4.0k
views
GC content of 10x Genomics
fastqc 10x GC content
updated 3.7 years ago by ▴ 180 • written 5.0 years ago by ★ 1.8k
0
votes
16
replies
2.8k
views
How to convert ncbi gff file to ensembl gff format
bcftools gff
updated 13 months ago by 43k • written 20 months ago by ▴ 10
1
vote
16
replies
2.0k
views
Why I see very high mapping percentage, Is this normal or anything wrong in generating libraries?
RNA-Seq hisat2 samtools mapping
updated 5.9 years ago by 20 • written 6.0 years ago by ▴ 770
7
votes
16
replies
3.9k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing genome-sequence fastqc genome sequence
4.1 years ago by Researcher ▴ 20
0
votes
16
replies
5.2k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools sort
10.9 years ago by chentong.biology ▴ 50
16
votes
16
replies
3.1k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
6.1 years ago by bioinfo456 ▴ 150
4
votes
16
replies
6.1k
views
How to count occurrence of numbers in text files using phython
python excel counting writelines
7.3 years ago by Kachibunny • 0
9
votes
16
replies
1.5k
views
I am trying to select some reference genome region of a bam file, but got an error
SAMTOOLS
updated 3.7 years ago by 15k • written 3.7 years ago by ▴ 160
9
votes
16
replies
3.8k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 13 months ago by 43k • written 5.7 years ago by ▴ 710
7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
7.7 years ago by aggregatibacter ▴ 180
4
votes
16
replies
4.5k
views
Working with human database in Kraken
RNA-Seq next-gen genome
7.9 years ago by Ron ★ 1.2k
1
vote
16
replies
7.0k
views
After sorting bam file not able to index ?
alignment next-gen
updated 5.2 years ago by 20 • written 5.3 years ago by ▴ 980
5
votes
16
replies
2.6k
views
a lot of OTUs wth no reference
16S
6.5 years ago by agata88 ▴ 870
15
votes
16
replies
1.7k
views
ncbi error report log for validate fastq issue
sra-tools
updated 7 months ago by 141k • written 7 months ago by ★ 1.2k
14
votes
16
replies
1.9k
views
Why are some mapped reads not mapped completely?
RNA-Seq mapping
updated 3.5 years ago by 15k • written 3.5 years ago by ▴ 80
0
votes
16
replies
3.2k
views
Problems with installation of Prodege decontamination software
genome next-gen sequencing sequence blast
updated 7.2 years ago by 20 • written 7.3 years ago by • 0
13
votes
16
replies
7.2k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
5.3 years ago by DNAngel ▴ 250
5
votes
16
replies
4.3k
views
plotting problem with loop in R
R plot
4.9 years ago by smyiz ▴ 30
13
votes
16
replies
6.1k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
7.3 years ago by Paul ★ 1.5k
2
votes
16
replies
1.9k
views
I want to know is it a true method ?
vcf SNP realignment
6.1 years ago by Siavash Salek Ardestani ▴ 20
2
votes
16
replies
10k
views
Tophat with Bowtie2 long index
tophat bowtie
updated 2.3 years ago by 43k • written 9.8 years ago by ▴ 140
5
votes
16
replies
6.2k
views
Remove duplicate lines based on specific columns
r python intersect reads
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 70
4
votes
16
replies
1.7k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools RNAseq samtools BAM
updated 9 weeks ago by 43k • written 7 months ago by • 0
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel R statistics
updated 11 months ago by 43k • written 5.1 years ago by ▴ 60
4
votes
16
replies
955
views
hisat2 location does not exist
hisat2
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling bcftools nf-core
10 months ago by Chris ▴ 260
5
votes
15
replies
2.1k
views
Sample contamination level over 30%
next-gen
6.6 years ago by haiying.kong ▴ 360
5
votes
15
replies
1.9k
views
Testing uniform distribution of SNPs across chromosome
uniform vcf SNP
5.0 years ago by misterie ▴ 110
2
votes
15
replies
1.5k
views
How to call all the allele in samples
SNP
6.0 years ago by Kritika ▴ 260
0
votes
15
replies
3.7k
views
Identify genes in a tophat aligned bam/sam file
blast alignment rna-seq gene
updated 16 months ago by 43k • written 8.9 years ago by • 0
5
votes
15
replies
1.5k
views
Get list of gene signatures published
bailey genes subtype pancreas
3.3 years ago by sabin ▴ 50
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
4 months ago by analyst ▴ 30
0
votes
15
replies
2.0k
views
compare two NCBI ftp tables
table NCBI
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 20
1
vote
15
replies
3.3k
views
How to perform multiple alignment using MAFFT?
genome alignment gene sequence
3.0 years ago by anikcropscience ▴ 230
11
votes
15
replies
2.8k
views
How do I get the read counts for a specific exon
bam exon
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 30
3
votes
15
replies
2.0k
views
Overlapping regions in a BED file
regions BED Sequence exons annotation
22 months ago by Matej • 0
1
vote
15
replies
2.7k
views
Copy Number Analysis on single file
CNV
updated 4.7 years ago by 87k • written 4.7 years ago by ▴ 130
2
votes
15
replies
2.2k
views
to get each covariate with PC loading in PCA
RNA-seq PCA
5.3 years ago by Grace_G ▴ 20
2
votes
15
replies
4.6k
views
Error when indexing a bcf file
vcf bcf
5.7 years ago by Famf ▴ 30
0
votes
15
replies
2.4k
views
pathway analysis tools for xenopus
pathways omics xenopus
updated 7.8 years ago by 7.5k • written 7.8 years ago by ▴ 90
6
votes
15
replies
2.4k
views
processing in strelka2 with multiples bam file in directory
strelka2
updated 2.3 years ago by ▴ 70 • written 4.4 years ago by ▴ 230
3
votes
15
replies
2.3k
views
RNA Seq Analysis:Feature Counts are zero
RNA-Seq feature counts
updated 3.9 years ago by 20 • written 3.9 years ago by ▴ 20
1
vote
15
replies
4.4k
views
Ultrafast alignment of short sequences to a genome (with up to 5 mismatches!)
genome alignment
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 360
1
vote
15
replies
1.5k
views
How to reduce my dataset in order to plot it?
correlation igraph
updated 4.7 years ago by 20 • written 4.9 years ago by ▴ 300
1
vote
15
replies
3.6k
views
Install Lefse in Ubuntu 12
install lefse microbiome
5.8 years ago by goh ▴ 10
6
votes
15
replies
1.6k
views
Reads partly within an exon
RNA-Seq
6.8 years ago by benjyrolls ▴ 70
4
votes
15
replies
3.3k
views
Adding Multiple readgroups to BAM file
GATK ReadGroups
8.0 years ago by vakul.mohanty ▴ 270
1,000 results • Page 4 of 20
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Answer: Missing protein (VEGF-A) in String db
Missing protein (VEGF-A) in String db
Comment: Sequence read length shorter than flow cell specification
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
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Answer: Rare Disease Variant Pathway Analysis by LauferVA 4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification by swbarnes2 14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package by DKA ▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis by ATpoint 82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets by ATpoint 82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis by kilcdincer ▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases by GenoMax 141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases by 5heikki 11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : ```r Idents(seuObj) <- 'RNA_snn_res.0.1' ``` You may wrongly assign other value to it such as `…
Answer: ScRNAseq-How to correctly choose cell type marker genes by Bioinfotec ▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question by Bioinfotec ▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification by GenoMax 141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing by rohitsatyam102 ▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
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