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1,000 results • Page 2 of 20
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1
vote
12
replies
1.2k
views
Volcano plot interpretation
EnhancedVolcano volcano-plot
updated 3 months ago by 39k • written 22 months ago by ▴ 20
2
votes
12
replies
1.4k
views
The best way to get gene lengths for 15K+ genes?
r EDAseq RNA-seq
8 months ago by JACKY ▴ 80
0
votes
12
replies
1.6k
views
bedtools intersect issue
bed bedtools
updated 9 weeks ago by 39k • written 4.8 years ago by ▴ 120
2
votes
12
replies
635
views
how to align an intron from a complex
genomic
updated 11 months ago by 47k • written 11 months ago by • 0
1
vote
12
replies
3.2k
views
dN/dS analysis of genomes
genome sequence alignment
7 months ago by Mehmet ▴ 800
7
votes
12
replies
840
views
Integrated genes from bulk RNA seq and ATAC seq
bulk-RNA integrated ATAC-seq
updated 5 days ago by ▴ 180 • written 12 days ago by ▴ 100
0
votes
12
replies
2.3k
views
Tax4Fun2 - error
tax4fun silva blast
updated 9 months ago by 129k • written 15 months ago by ▴ 10
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 7 months ago by 39k • written 7.8 years ago by ★ 1.8k
2
votes
12
replies
1.8k
views
Nothing will align with HTSeq?
RNA-Seq htseq
updated 8 months ago by 39k • written 7.7 years ago by ▴ 620
6
votes
12
replies
1.2k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r biomarker
updated 10 weeks ago by 39k • written 4.3 years ago by ▴ 290
5
votes
12
replies
630
views
Data from an experiment
single-cell
updated 3 months ago by 129k • written 3 months ago by ▴ 100
1
vote
12
replies
3.2k
views
How to run multiple alignment and SNP-calling of WGS data in .gb and .fasta using Python or Ruby/Java or any free software?
alignment sequencing software
updated 11 months ago by 39k • written 8.1 years ago by ▴ 60
6
votes
12
replies
1.3k
views
VCF files 101 - for people from non Bioinformatics Background
vcf sequencing genome variant-calling
updated 11 weeks ago by 39k • written 2.8 years ago by ▴ 20
2
votes
12
replies
896
views
how to get to a VCF from bam files
Mpileup Samtools BAM bcftools VCF
updated 9 weeks ago by 39k • written 9 weeks ago by • 0
1
vote
12
replies
3.7k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq alignment sequencing
updated 4 months ago by 72k • written 5.7 years ago by ▴ 170
8
votes
12
replies
2.7k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 10 weeks ago by 39k • written 21 months ago by ▴ 30
0
votes
12
replies
2.7k
views
Allpaths- Keep getting ConvertToFastbQualb.pl failed for group 'paired_ends' when I run PrepareAllPaths
next-gen Assembly
updated 5 months ago by 39k • written 7.9 years ago by ▴ 80
2
votes
12
replies
4.2k
views
Adding barcodes to forward and reverse reads after sequencing
obitools barcoding next-gen-sequencing
updated 3 months ago by 39k • written 8.1 years ago by ▴ 20
4
votes
12
replies
1.0k
views
Bulk RNA seq: all p adjusted are the same
p-adj RNA-seq differential-gene-expression
updated 5 months ago by 39k • written 12 months ago by ▴ 10
0
votes
12
replies
2.9k
views
comparative analysis of two strains of bacteria's genomes
genome gene
updated 13 days ago by 39k • written 5.6 years ago by ▴ 20
6
votes
12
replies
560
views
Help with error in cellranger
Cellranger
updated 13 days ago by 129k • written 14 days ago by ▴ 100
4
votes
11
replies
6.5k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF snp
9 months ago by prasundutta87 ▴ 650
0
votes
11
replies
874
views
Problem with Trimmomatic Multiple Paired-End sequencing.
Trimmomatic
updated 4 months ago by 129k • written 4 months ago by • 0
0
votes
11
replies
2.4k
views
mpiBLAST Score and E-value Calculation
blast sequence
updated 12 months ago by 39k • written 8.2 years ago by • 0
1
vote
11
replies
3.0k
views
merge samples in phyloseq returns NAs
R phyloseq biom
updated 6 months ago by • 0 • written 2.9 years ago by ▴ 10
6
votes
11
replies
913
views
Calculate RPKM
RPKM
10 weeks ago by Chris ▴ 100
0
votes
11
replies
904
views
Python - Samtools mpileup find snps with allele frequency
snp mpileup python samtools
11 months ago by pablosolar.r ▴ 20
5
votes
11
replies
3.1k
views
Convert Plink to Arlequin
software-error plink Arlequin PGDSpider
updated 11 weeks ago by 39k • written 5.1 years ago by ▴ 30
1
vote
11
replies
3.0k
views
bedtools fisher interpretation of "in -a" "not in -b"
fisher bedtools intersection
updated 3 months ago by 39k • written 5.3 years ago by ▴ 720
4
votes
11
replies
2.6k
views
7 follow
Getting coding sequence length
NCBI Gene CDS
updated 11 months ago by ▴ 360 • written 2.9 years ago by ★ 4.2k
8
votes
11
replies
1.3k
views
using STAR instead of HISAT2
STAR
updated 10 months ago by 39k • written 10 months ago by ▴ 100
3
votes
11
replies
888
views
RepeatMasker error
repeatmasking transciptome RNA-seq
updated 10 months ago by ★ 1.8k • written 10 months ago by ▴ 110
0
votes
11
replies
1.5k
views
Error in Importing data in qiime2
Metagenomics Sequencing Qiime2 Amplicon
10 months ago by Vaishnavi • 0
4
votes
11
replies
1.1k
views
Running STAR
STAR
10 months ago by Chris ▴ 100
5
votes
11
replies
6.4k
views
Error while running miso
RNA-Seq splicing
updated 10 months ago by 39k • written 7.8 years ago by ▴ 40
10
votes
11
replies
8.3k
views
How to adjust my manhattan plot to look better?
qqman manhattan R
updated 12 months ago by 39k • written 8.2 years ago by ▴ 40
4
votes
11
replies
2.7k
views
Please add an explicit type tag :NAME
software-error next-gen genome
updated 3 months ago by 39k • written 5.1 years ago by ▴ 30
0
votes
10
replies
807
views
using txt file to pass pathways for pipelines
muscle seqkit bash fasta
updated 10 months ago by 39k • written 10 months ago by • 0
7
votes
10
replies
1.2k
views
col as names [solved]
R
updated 10 weeks ago by 39k • written 4.2 years ago by ▴ 90
5
votes
10
replies
891
views
How to change chromosome names in assembly fasta downloaded from NCBI?
grch38 ncbi grch37 fasta
8 months ago by magnolia ▴ 20
2
votes
10
replies
687
views
Can I directly compare the regions defined by peaks from pair-end 50 and pair-end 100 ATAC-seq?
ATAC-seq
updated 8 months ago by 72k • written 8 months ago by ▴ 120
3
votes
10
replies
969
views
Error with FindConservedMarkers()
FindConservedMarkers
3 months ago by Chris ▴ 100
2
votes
10
replies
963
views
R-studio freezes error
RStudio offtopic
updated 7 months ago by 39k • written 7 months ago by ▴ 140
1
vote
10
replies
2.5k
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 3 days ago by 39k • written 4.2 years ago by ▴ 100
1
vote
10
replies
2.4k
views
Issue in running viroBlast from localhost
blast php viroBlast javascript sequence
updated 10 months ago by 39k • written 7.3 years ago by ▴ 10
0
votes
10
replies
6.9k
views
Error: reads file does not look like a fastq file
fastq bowtie2 ChIP-Seq
updated 10 weeks ago by 39k • written 6.7 years ago by ▴ 40
2
votes
10
replies
1.0k
views
Running salmon in alignment mode?
transcriptomics salmon metatranscriptomics rna rna-seq
11 months ago by pearl2070 ▴ 10
1
vote
10
replies
1.3k
views
Weird results for scRNA-seq
scRNA-seq GEO
updated 5 months ago by ▴ 70 • written 5 months ago by ▴ 100
5
votes
10
replies
4.6k
views
Antisense transcription - how to detect it?
RNA-Seq antisense
updated 9 months ago by 39k • written 7.6 years ago by 13k
0
votes
10
replies
2.3k
views
eXpress error gene length different
eXpress rna-seq
updated 10 months ago by 39k • written 8.1 years ago by ▴ 550
1,000 results • Page 2 of 20
Recent Votes
Comment: Regular Expression for conversion
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
A: PolyPhen Humdiv vs HumVar discrepancies
A: How To Get Annotation For Bed File From Another Bed File
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Recent Replies
Comment: Unusual FASTQ file by Ram 39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ? by bhumm ▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data? by swbarnes2 13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file by bhumm ▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline by ATpoint 72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline by swbarnes2 13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline by Ram 39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline by turcoa1 • 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline by Ram 39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline by turcoa1 • 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree by GenoMax 129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline by Ram 39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index by ashleymb1116 • 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index by GenoMax 129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
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