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1,000 results • Page 4 of 20
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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
11.0 years ago by chentong.biology ▴ 50
0
votes
16
replies
3.8k
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
1.6k
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
2.0k
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
3
votes
16
replies
4.1k
views
GC content of 10x Genomics
fastqc 10x GC content
updated 3.7 years ago by ▴ 180 • written 5.1 years ago by ★ 1.8k
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
6.1 years ago by Siavash Salek Ardestani ▴ 20
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
4
votes
16
replies
1.0k
views
hisat2 location does not exist
hisat2
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
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
4
votes
16
replies
1.8k
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
7
votes
16
replies
3.6k
views
How do I get a GFF file
snp
4.9 years ago by apl00028 ▴ 90
0
votes
16
replies
4.6k
views
Issue using MaSuRCA-3.2.6
Assembly assembler
updated 5.7 years ago by 20 • written 5.9 years ago by ▴ 130
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
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
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
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
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
8.7k
views
STAR - genome indexes generation, genome file not created
RNA-Seq star
updated 4.7 years ago by 20 • written 7.5 years ago by ▴ 70
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
15
votes
16
replies
1.7k
views
ncbi error report log for validate fastq issue
sra-tools
updated 7 months ago by 142k • written 7 months ago by ★ 1.2k
5
votes
16
replies
2.7k
views
How to extract intron counts from total RNA Sequencing?
featurecounts RNAseq htseq STAR
17 months ago by PK ▴ 130
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
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
15
replies
4.0k
views
Paired-read alignment length from BAM/SAM file
bam sam paired-read alignment
6.9 years ago by Soumitra Pal ▴ 10
5
votes
15
replies
1.6k
views
NGS Sequencing depths
next-gen sequencing gene
7.2 years ago by sliproach ▴ 10
7
votes
15
replies
4.3k
views
Biopython Pairwise Alignment output
biopython needleman global alignment
4.1 years ago by tommaso.green • 0
3
votes
15
replies
3.2k
views
Less and less genes predicted with each iteration of SNAP/MAKER
maker annotation snap gene prediction genomics
updated 2.6 years ago by ▴ 20 • written 4.1 years ago by ▴ 30
5
votes
15
replies
1.5k
views
Get list of gene signatures published
bailey genes subtype pancreas
3.3 years ago by sabin ▴ 50
1
vote
15
replies
6.0k
views
How to Extract Specific Region on Bam file
Nanopore HG38 Rna-Seq Genome
updated 2.9 years ago by 87k • written 2.9 years ago by ▴ 40
6
votes
15
replies
2.5k
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
5
votes
15
replies
2.2k
views
Is this a valid analysis?
geo rankprod analysis microarray
7.5 years ago by randalljellis ▴ 90
1
vote
15
replies
1.6k
views
Single Cell RNA Seq
scTransform Harmony scRNAseq Seurat
8 months ago by scRNA2023 • 0
20
votes
15
replies
30k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink SNP
updated 21 months ago by 43k • written 8.3 years ago by ▴ 200
2
votes
15
replies
1.6k
views
from protein to tRNA combinations
RNA-Seq rna-seq
written 3.4 years ago by • 0
5
votes
15
replies
5.4k
views
Annotation with snpEFF
annotation vcf snpeff extractFields
updated 5.8 years ago by 20 • written 5.9 years ago by ▴ 960
6
votes
15
replies
1.6k
views
The Best Cloud Solution For Genomics
cloud data-sharing genomics workflow
updated 21 months ago by 43k • written 22 months ago by ▴ 50
1
vote
15
replies
3.7k
views
Install Lefse in Ubuntu 12
install lefse microbiome
5.9 years ago by goh ▴ 10
0
votes
15
replies
2.2k
views
Chromosome accession numbers correspond to which chromosome?
bam chromosome bed
18 months ago by amy__ ▴ 160
10
votes
15
replies
6.2k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast MEGAN6 Taxonomy DIAMOND
7.4 years ago by Farbod ★ 3.4k
0
votes
15
replies
3.3k
views
bcftools multiple samples
snp
4.5 years ago by evelyn ▴ 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
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
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
0
votes
15
replies
2.6k
views
Strategy for generating a consensus sequence for 100 complete bacterial genomes?
consensus seq mauve
5.9 years ago by Alec Watanabe ▴ 60
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
Recent Votes
Comment: Bacterial plasmid analysis
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
A: What is the difference between GRCh37 and hs37? And hg19?
A: Decoy In Reference Assembly
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Recent Replies
Answer: How goes gene length effect the number of reads mapped by i.sudbery 19k
See my answer about the what hows and whens of RNA-seq normalisation here: https://www.biostars.org/p/9586553/#9586566
Comment: What purposes can TPM values be used for? by dsull ★ 5.9k
Since you have mutant vs wild-type, using DESeq2 is the right thing to do. Rather than showing a small table of numbers, you should make a …
Answer: What purposes can TPM values be used for? by i.sudbery 19k
See my post here for more details on RNA-seq normalisation: https://www.biostars.org/p/9586553/#9586566 In short, TPM normalises for ge…
Comment: Bacterial plasmid analysis by Zamin Iqbal • 0
I vote for this, it's the best! (but also, I am Daria's PhD supervisor so I am biased). Preprint out soon(ish) [no pressure Daria!]
Comment: Downsampling long-read BAM files by GenoMax 142k
Is this what you used ultimately? Did this tool satisfy the "specific average depth" requirement? You could accept (green check mark) this…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by Estevão • 0
Thank you. My budget is around 20 thousand dollars.
Answer: Problem with data downloaded from Short Reads Archive (SRA) by atharvakarkare14 ▴ 20
Prefetch files using sratoolkit **prefetch** command and then use **fasterq-dump**. There you can see the number of reads. For validation, …
Answer: Downsampling long-read BAM files by eesiribloom ▴ 80
random downsampling of bam files is now possible using [rasusa][1] [v1.0.0][2] with the `aln` subcommand [1]: https://github.com/mbh…
Comment: Problem with data downloaded from Short Reads Archive (SRA) by GenoMax 142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA) by ATpoint 82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
Answer: What analysis suitable to identify similarly expressed genes between two samples by ATpoint 82k
DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
Comment: RNAseq one control two conditions, shared and exclusive genes by Mohamed Abderrahmane ▴ 20
In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA) by Begonia_pavonina ▴ 150
Thank you @atpoint, I did already investigate this error on the DADA2 github. It seems that the "BiocParallel" error can be due to multipl…
Comment: Discrepancy in read counts from fastq by GenoMax 142k
Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
Comment: Problem with data downloaded from Short Reads Archive (SRA) by ATpoint 82k
One cannot help you with this. The error is from R, yet you show not a single line of R code.
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