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1,000 results • Page 4 of 20
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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 141k • written 7 months ago by ★ 1.2k
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
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
3.6k
views
How do I get a GFF file
snp
4.8 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
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length Bed
updated 10 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
5.3 years ago by Moses ▴ 150
2
votes
16
replies
3.1k
views
Enhancing draft genome using 10X data
10X draft_genome Assembly
5.7 years ago by Mostafa ▴ 20
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
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 7.4 years ago by ▴ 70
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
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene next-gen
4.3 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
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
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
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
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
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
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
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
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
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
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
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
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
0
votes
15
replies
2.1k
views
Chromosome accession numbers correspond to which chromosome?
bam chromosome bed
18 months ago by amy__ ▴ 160
0
votes
15
replies
3.3k
views
bcftools multiple samples
snp
4.5 years ago by evelyn ▴ 230
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
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
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
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
1.5k
views
Get list of gene signatures published
bailey genes subtype pancreas
3.3 years ago by sabin ▴ 50
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
7
votes
15
replies
7.1k
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
0
votes
15
replies
3.2k
views
SAMFormatException: Did not inflate expected amount error
WES
updated 2.5 years ago by ▴ 20 • written 2.8 years ago by ▴ 20
6
votes
15
replies
2.7k
views
Why can't I reproduce the same heat map
ggplots R RNA-Seq
updated 5.7 years ago by 20 • written 5.8 years ago by ▴ 140
6
votes
15
replies
8.4k
views
Strand specific protocol for bowtie2 alignment
bowtie2 rnaseq alignment RNA-Seq
updated 2.4 years ago by 43k • written 8.5 years ago by ▴ 100
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
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
2
votes
15
replies
4.2k
views
How to interpret reads mapped to genome from samtools flagstat vs TopHat align_summary.txt ?
RNA-Seq
8.0 years ago by Vasu ▴ 770
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
7
votes
15
replies
2.2k
views
very low coverage when mappin genomic DNA
mapping coverage DNA genomic
updated 2.7 years ago by 82k • written 2.7 years ago by ★ 1.2k
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
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
4
votes
15
replies
3.3k
views
Adding Multiple readgroups to BAM file
GATK ReadGroups
8.0 years ago by vakul.mohanty ▴ 270
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
1,000 results • Page 4 of 20
Recent Votes
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
Answer: Differential Expression using Isoseq-supplemented reference transcriptome by Gordon Smyth ★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Answer: Finding batch and outlayers by Tigran • 0
![enter image description here][1] [1]: /media/images/aa60b9ef-b08c-4093-9f0d-fb656a5c
Comment: NGS forensics: how to know if data is fabricated by benformatics 3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated by benformatics 3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue by noodle ▴ 540
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue by Mensur Dlakic ★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated by Mensur Dlakic ★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
I think you might be getting stuck on less relevant parts of my exercise. The most important point was that nothing is wrong with the data.…
Comment: What does it mean single base resolution in sequencing? by dsull ★ 5.9k
Great comprehensive explanation and overview of the technologies -- with regards to sequencing assays, the one thing I'd add is SNV identif…
Answer: What does it mean single base resolution in sequencing? by dsull ★ 5.9k
I think that term means slightly different things in different contexts. For example, it's useful to profile mRNA modifications (e.g. m6a) …
Comment: Cannot process all the reads in a fast5 file? by chujie • 0
Hi, I met the same problem, have you found the solution?
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