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1,000 results • Page 4 of 20
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7
votes
16
replies
21k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq rna-seq
7.8 years ago by aggregatibacter ▴ 180
3
votes
16
replies
4.1k
views
GC content of 10x Genomics
fastqc 10x GC content
updated 3.8 years ago by ▴ 180 • written 5.1 years ago by ★ 1.8k
13
votes
16
replies
6.1k
views
Mask or trim primer sequences in Amplicon sequencing
amplicon mask trimming fastq
7.4 years ago by Paul ★ 1.5k
0
votes
16
replies
5.2k
views
Unable To Delete Tmp Files Of Samtools Sort
samtools sort
11.0 years ago by chentong.biology ▴ 50
0
votes
16
replies
3.9k
views
Gff to genbank - feature is missing
DNA augustus gff3 genbank
updated 11 months ago by 43k • written 5.9 years ago by ▴ 10
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length Bed
updated 11 months ago by 43k • written 4.3 years ago by ▴ 500
3
votes
16
replies
3.5k
views
FastTree trifurcating Root node
alignment FastTree Phylogenetic Tree
5.4 years ago by Moses ▴ 150
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 3.8 years ago by 15k • written 3.8 years ago by ▴ 160
2
votes
16
replies
3.1k
views
Enhancing draft genome using 10X data
10X draft_genome Assembly
5.8 years ago by Mostafa ▴ 20
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene next-gen
4.4 years ago by Chaimaa ▴ 260
9
votes
16
replies
1.9k
views
feature extraction from SNPs in R
R gene sequence SNP
5.5 years ago by bioinfo456 ▴ 150
0
votes
16
replies
3.2k
views
Problems with installation of Prodege decontamination software
genome next-gen sequencing sequence blast
updated 7.3 years ago by 20 • written 7.3 years 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 5.2 years ago by ▴ 60
7
votes
16
replies
4.0k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing genome-sequence fastqc genome sequence
4.1 years ago by Researcher ▴ 20
3
votes
16
replies
1.6k
views
Problem, getting information only from the last row and not from all the rows
perl
6.1 years ago by ArusjakGevorgyan ▴ 30
0
votes
16
replies
2.9k
views
How to convert ncbi gff file to ensembl gff format
bcftools gff
updated 14 months ago by 43k • written 20 months ago by ▴ 10
5
votes
16
replies
2.8k
views
How to extract intron counts from total RNA Sequencing?
featurecounts RNAseq htseq STAR
18 months ago by PK ▴ 130
5
votes
16
replies
2.7k
views
a lot of OTUs wth no reference
16S
6.6 years ago by agata88 ▴ 870
9
votes
16
replies
3.9k
views
6 follow
covert SAM to full length fasta
fasta SAM
updated 14 months ago by 43k • written 5.7 years ago by ▴ 710
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 6.0 years ago by 20 • written 6.1 years ago by ▴ 770
4
votes
16
replies
1.0k
views
hisat2 location does not exist
hisat2
updated 11 weeks ago by 43k • written 12 weeks ago by • 0
7
votes
16
replies
2.8k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq sequencing
updated 13 months ago by 43k • written 6.6 years ago by ★ 3.6k
16
votes
16
replies
3.2k
views
Using DESeq2 results for building a classifier
deseq2 RNA-Seq differentially expressed genes
6.1 years ago by bioinfo456 ▴ 150
2
votes
16
replies
1.9k
views
I want to know is it a true method ?
vcf SNP realignment
6.2 years ago by Siavash Salek Ardestani ▴ 20
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
2
votes
16
replies
10k
views
Tophat with Bowtie2 long index
tophat bowtie
updated 2.4 years ago by 43k • written 9.8 years ago by ▴ 140
14
votes
16
replies
2.0k
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
4
votes
16
replies
1.9k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools RNAseq samtools BAM
updated 11 weeks ago by 43k • written 7 months ago by • 0
0
votes
15
replies
3.3k
views
how to make a .bam file from fastQ for RNA-seq ion torrent with BBmap
RNA-Seq
6.6 years ago by genya35 ▴ 40
6
votes
15
replies
3.1k
views
Why GSVA returns a matrix with fewer gene-sets?
microarray GSVA
updated 2.4 years ago by ▴ 70 • written 6.2 years ago by ▴ 280
2
votes
15
replies
1.2k
views
Manipulate refseq database
ncbi database nt refseq
updated 4.3 years ago by 20 • written 4.3 years ago by ▴ 80
11
votes
15
replies
2.9k
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
6
votes
15
replies
8.5k
views
Strand specific protocol for bowtie2 alignment
bowtie2 rnaseq alignment RNA-Seq
updated 2.5 years ago by 43k • written 8.5 years ago by ▴ 100
3
votes
15
replies
5.6k
views
Pairwise sequence alignment with Biojava?
sequence-alignment biojava java
updated 2.3 years ago by 43k • written 9.5 years ago by ▴ 360
0
votes
15
replies
2.4k
views
pathway analysis tools for xenopus
pathways omics xenopus
updated 7.9 years ago by 7.5k • written 7.9 years ago by ▴ 90
1
vote
15
replies
3.7k
views
Can I use PICARD (SortSam) instead of SAMTOOLS (sort) for sorting bam files in RNAseq pipeline where HISAT2 is used for alignment.
RNA-Seq software error sequencing next-gen
6.0 years ago by shuksi1984 ▴ 60
3
votes
15
replies
2.4k
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
0
votes
15
replies
3.3k
views
bcftools multiple samples
snp
4.5 years ago by evelyn ▴ 230
1
vote
15
replies
3.7k
views
Fastx quality filter
next-gen RNA-Seq software error sequencing
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast MEGAN6 Taxonomy DIAMOND
7.5 years ago by Farbod ★ 3.4k
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
6
votes
15
replies
1.6k
views
The Best Cloud Solution For Genomics
cloud data-sharing genomics workflow
updated 22 months ago by 43k • written 23 months ago by ▴ 50
7
votes
15
replies
2.1k
views
cufflinks in loop
rna-seq RNA-Seq genome
updated 5.9 years ago by 16k • written 5.9 years ago by • 0
1
vote
15
replies
4.4k
views
Ultrafast alignment of short sequences to a genome (with up to 5 mismatches!)
genome alignment
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 360
7
votes
15
replies
7.2k
views
6 follow
blastn error - NCBI C++ Exception
assembly blast alignment
updated 2.1 years ago by 15k • written 3.1 years ago by ▴ 980
6
votes
15
replies
1.6k
views
Reads partly within an exon
RNA-Seq
6.8 years ago by benjyrolls ▴ 70
8
votes
15
replies
2.0k
views
RNAseq differential expression analysis : no significative FDR but significative GO enrichment
RNA-Seq differential expression
4.6 years ago by guillaume.rbt ★ 1.0k
1
vote
15
replies
3.4k
views
How to perform multiple alignment using MAFFT?
genome alignment gene sequence
3.1 years ago by anikcropscience ▴ 230
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
4.1k
views
Bowtie2 error :: (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
next-gen SNP alignment
updated 4.1 years ago by ▴ 560 • written 4.1 years ago by ▴ 10
1,000 results • Page 4 of 20
Recent Votes
A: ensembl gene id
A: How to deal with the case that one gene symbol matches multiple ensembl ids?
Answer: DESeq2 error
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Comment: How to calculate coverage of Nanopore long read data?
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
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Recent Replies
Comment: How to extract cells of different species after mapping with combined genome? by GenoMax 142k
You have used the tag `snRNAseq`. I am not familiar with singleron tech but if you have sequence data you may be able to use `xenome` or `b…
Comment: bbmerge (bbmap) ~ error with insert size file output by GenoMax 142k
It may be best to go back to the original data and then do `bbmerge.sh` on it to get original insert size estimates (before any operations …
Comment: bbmerge (bbmap) ~ error with insert size file output by chrisk • 0
Hi Brian, Thank you and apologies for the extra future revision works. Out of curiosity we disabled neural networks 'nn=f' and the file o…
Comment: bbmerge (bbmap) ~ error with insert size file output by chrisk • 0
Hi Genomax, This is the thread: https://www.biostars.org/p/9582467/ Cheers, Chris
Comment: Inquiry about deseq2 transformation by Chen • 0
that's helpful, thanks :)
Comment: bbmerge (bbmap) ~ error with insert size file output by Brian Bushnell 20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
Comment: Annotating file using bcftools by kl ▴ 10
Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
Comment: Filtering VCF files based on VAF giving incorrect results by Arton ▴ 10
These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
Answer: Calculate allelic frequency from VEP output vcf file by ramiro.barrantes • 0
Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
Comment: Using VEP annotation output as the input for a second VEP annotation by Ram 43k
That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 120
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
Comment: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas by Ash ▴ 10
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
Comment: Doubt about the process of annotation, detection, identification and classificat by MarcosCosta • 0
Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
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