Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
0
votes
4
replies
1.9k
views
Ran dipSpades for a diploid fungus genome -- now what?
diploid genome assembly dipspades
updated 3.6 years ago by 20 • written 6.6 years ago by ▴ 200
3
votes
11
replies
16k
views
SPAdes is running out of memory
spades hybrid assembly fungi memory
updated 3.7 years ago by • 0 • written 6.7 years ago by ▴ 200
0
votes
3
replies
2.7k
views
SPAdes error code -6
SPAdes metagenomics Assembly
4.8 years ago by Lina F ▴ 200
2
votes
4
replies
2.2k
views
How does bbduk calculate it's memory requirements?
bbduk docker memory
4.9 years ago by Lina F ▴ 200
2
votes
5
replies
1.7k
views
Error building snpEff database "Transcript 'hypothetical_protein' already exists"
snpeff database build
updated 13 months ago by • 0 • written 5.8 years ago by ▴ 200
2
votes
6
replies
2.7k
views
Running two bedtools commands in series produces error "has non positional records"
bedtools vcf
5.8 years ago by Lina F ▴ 200
3
votes
2
replies
3.3k
views
Jellyfish: every other kmer count is zero
kmer counting jellyfish genome size estimation
5.9 years ago by Lina F ▴ 200
0
votes
4
replies
2.8k
views
Visualizing whole genome alignment beyond dotplots
dotplot visualization alignment whole genome
updated 6.2 years ago by 35k • written 6.2 years ago by ▴ 200
4
votes
2
replies
4.2k
views
Removing common SNPs from a set of VCF files
SNP vcf filtering
6.5 years ago by Lina F ▴ 200
1
vote
3
replies
4.6k
views
How to filter SNPs after Freebayes, if at all, in a fungal haploid genome alignment?
freebayes SNP filtering
6.6 years ago by Lina F ▴ 200
3
votes
4
replies
3.4k
views
Align two microbial genomes -- is mummer still the way to go?
genome alignment mummer nucmer snps vcf
6.7 years ago by Lina F ▴ 200
0
votes
0
replies
1.3k
views
Upcoming workshops tackling data analysis of hybrid sequencing technologies?
nanopore minion workshop hybrid sequencing
6.7 years ago by Lina F ▴ 200
6
votes
9
replies
8.0k
views
How to get fasta sequences of features from a GFF3 file?
gff3 fasta parser
updated 6.8 years ago by 10k • written 6.8 years ago by ▴ 200
1
vote
8
replies
5.0k
views
Demultiplexing reads from two libraries (single and dual indices) that were sequenced in the same sequencing run
demultiplexing nextseq bcl2fastq
updated 6.8 years ago by 35k • written 6.8 years ago by ▴ 200
6
votes
5
replies
4.7k
views
How to assemble complex soil metagenome datasets?
metagenomics assembly soil
updated 6.8 years ago by 21k • written 6.8 years ago by ▴ 200
0
votes
1
reply
1.3k
views
Capturing whole gene sequences from WGS metagenomics sample
metagenomics assembly contigs binning
updated 6.9 years ago by 5.3k • written 6.9 years ago by ▴ 200
0
votes
0
replies
2.4k
views
Statistical approach to identifying outliers in RNAseq data?
RNA-Seq outliers detection statistics
7.0 years ago by Lina F ▴ 200
6
votes
2
replies
3.2k
views
Calling SNPs with samtools: how to specify how many supporting observations are required?
samtools variant calling snps freebayes
updated 7.0 years ago by 20k • written 7.0 years ago by ▴ 200
0
votes
2
replies
1.2k
views
RNAseq transcript quantification: how to deal with different number of genes in host organism?
RNA-Seq sailfish quantification transcripts R
updated 7.0 years ago by 35k • written 7.0 years ago by ▴ 200
1
vote
4
replies
2.3k
views
Best reference database for 16S soil datasets?
metagenomics soil reference 16S
updated 7.1 years ago by ★ 5.2k • written 7.1 years ago by ▴ 200
1
vote
4
replies
1.6k
views
How to assess biases in ribosomally depleted RNAseq data?
RNA-Seq bias transcripts
7.2 years ago by Lina F ▴ 200
0
votes
0
replies
1.7k
views
How does RNA-SeQC calculate the "Mean CV" value?
RNA-Seq qc coefficient of variation
7.2 years ago by Lina F ▴ 200
0
votes
0
replies
2.5k
views
How to format input data for Picard CollectRnaSeqMetrics
picard RNA-Seq gtf
updated 7.3 years ago by 161k • written 7.3 years ago by ▴ 200
0
votes
2
replies
1.9k
views
RNA-SeQC does not calculate information about "Strand Specificity"
RNA-Seq qc
updated 7.3 years ago by 8.2k • written 7.3 years ago by ▴ 200
3
votes
2
replies
3.2k
views
Yeast GTF file needed for RNA-SeQC run
qc gtf yeast RNA-Seq RNA-SeQC
updated 7.3 years ago by ▴ 600 • written 7.3 years ago by ▴ 200
4
votes
6
replies
6.1k
views
bwa mem: which parameters to tune to improve alignment?
bwa parameters tuning
7.4 years ago by Lina F ▴ 200
1
vote
2
replies
3.0k
views
Generating consensus sequences
consensus fasta bwa vcftools
updated 7.4 years ago by ▴ 290 • written 7.4 years ago by ▴ 200
0
votes
1
reply
1.6k
views
FreeBayes does not deal with ambiguous nucleotides -- what are good alternatives?
freebayes open source SNP
7.5 years ago by Lina F ▴ 200
6
votes
6
replies
8.4k
views
Cannot find downloaded files from SRA toolkit (prefetch)
prefetch sratoolkit
updated 10 months ago by 43k • written 7.5 years ago by ▴ 200
1
vote
2
replies
1.4k
views
Do I need to explicitly remove rRNA from E. coli RNAseq data?
rrna rnaseq ecoli transcriptomics
7.5 years ago by Lina F ▴ 200
0
votes
2
replies
4.1k
views
How to demultiplex 16S PE Miseq reads?
miseq demultiplex fastq 16S paired end reads
7.8 years ago by Lina F ▴ 200
0
votes
1
reply
1.4k
views
Microbiome data: Should unmatched reads be included in Shannon Diversity calculations?
microbiome shannon diversity unmatched reads
8.2 years ago by Lina F ▴ 200
2
votes
1
reply
3.6k
views
Extracting more features from EMBL files with Biopython
embl biopython
updated 18 months ago by 43k • written 8.8 years ago by ▴ 200
2
votes
3
replies
2.3k
views
How to incorporate metadata in 16S amplicon study and identify confounding variables
amplicon confounders 16S
updated 16 months ago by 43k • written 8.9 years ago by ▴ 200
8
votes
8
replies
4.4k
views
Is the order of records in the bam file produced by bwa the same as the order in the input fastq file?
mem fastq bwa aln sampe
updated 3.1 years ago by 43k • written 9.5 years ago by ▴ 200
35 results • Page 1 of 1
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6