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1
vote
7
replies
1.9k
views
Core_nt database not available to download?
blast ncbi
updated 8 months ago by 151k • written 8 months ago by ▴ 250
4
votes
6
replies
1.3k
views
How to check if all read names are paired properly in paired end fastq.gz files?
samtools illumina paired-end
updated 9 months ago by 4.9k • written 9 months ago by ▴ 250
1
vote
3
replies
916
views
Why is DESeq2 normalization making my top feature have identical values across samples?
DESEQ2 WGCNA
13 months ago by DNAngel ▴ 250
0
votes
0
replies
261
views
Should I keep taxa that have 0 counts when calculating alpha diversity?
Shannon-Weiner
13 months ago by DNAngel ▴ 250
0
votes
5
replies
1.3k
views
Samtools unmapped reads
samtools
2.2 years ago by DNAngel ▴ 250
0
votes
3
replies
2.1k
views
Samtools mapped and unmapped flags, what is the difference between the flags?
samtools
2.3 years ago by DNAngel ▴ 250
2
votes
2
replies
896
views
How do you get functional/biological role of motifs?
JASPAR
updated 2.3 years ago by 5.1k • written 2.3 years ago by ▴ 250
2
votes
8
replies
1.9k
views
How to get names and class information from a list of target IDs from the JASPAR database?
JASPAR
updated 2.3 years ago by 88k • written 2.3 years ago by ▴ 250
3
votes
3
replies
991
views
Program to detect cis-regulatory modules for a non model species?
factors transcription
2.5 years ago by DNAngel ▴ 250
4
votes
3
replies
1.3k
views
How do you find transcription factors in a newly sequenced genome?
interproscan factors transcription
updated 2.6 years ago by ▴ 20 • written 2.6 years ago by ▴ 250
7
votes
8
replies
1.6k
views
How do you obtain a list of transcription factors from a genome?
transcription-factor
updated 2.2 years ago by 45k • written 2.6 years ago by ▴ 250
0
votes
6
replies
4.7k
views
Confused about which database to use - nt or nr?
blast
updated 2.6 years ago by 11k • written 2.6 years ago by ▴ 250
0
votes
2
replies
905
views
What happened to the SparCC github repository?
sparcc
updated 3.1 years ago by ★ 2.1k • written 3.1 years ago by ▴ 250
2
votes
8
replies
4.4k
views
Why does Kraken2 not produce taxon percentages with --report flag?
kraken2
updated 3.4 years ago by ▴ 110 • written 4.0 years ago by ▴ 250
0
votes
0
replies
730
views
Can I use DESeq2 to analyze my abundance dataset, which also happens to have a lot of zeros?
deseq2
3.6 years ago by DNAngel ▴ 250
2
votes
4
replies
1.8k
views
WGCNA, what does it mean if no hub genes are identified?
WGCNA
3.6 years ago by DNAngel ▴ 250
1
vote
0
replies
709
views
R package for determining best model transformation for a dataset?
R
3.7 years ago by DNAngel ▴ 250
11
votes
15
replies
4.9k
views
Output of samtools view, what does the third column actually represent?
samtools
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 250
0
votes
0
replies
689
views
How to find out how many reads were used in contig assembly in metaSPADES?
metaspades
3.7 years ago by DNAngel ▴ 250
1
vote
1
reply
2.8k
views
How do you interpret Tukey's significance when there is no group clustering alone?
Tukey
3.7 years ago by DNAngel ▴ 250
1
vote
1
reply
1.8k
views
What is the difference between using -max_target_seqs 1 -max_hsps 1 versus just the defaults and then filtering for top hit?
blast
updated 3.7 years ago by 151k • written 3.7 years ago by ▴ 250
0
votes
0
replies
775
views
R vegdist does not compute distances for all my sites
vegan vegdist R
updated 3.7 years ago by 45k • written 3.7 years ago by ▴ 250
3
votes
1
reply
2.6k
views
What is the recommended contig length to filter?
metaspades
updated 3.8 years ago by ★ 29k • written 3.8 years ago by ▴ 250
2
votes
6
replies
1.4k
views
Is there a different names.dmp file in the taxonomy name/id browser?
ncbi
updated 3.8 years ago by 151k • written 3.8 years ago by ▴ 250
1
vote
11
replies
2.5k
views
Blast 2.11 not blasting all sequences in a file?
blast
3.9 years ago by DNAngel ▴ 250
7
votes
12
replies
2.4k
views
7 follow
Why do I lose sequences when converting my bam files into fastq?
fastq bam bamToFastq
updated 3.9 years ago by 14k • written 3.9 years ago by ▴ 250
0
votes
0
replies
832
views
Confused about sambamba syntax for unmapped and mapped
sambamba
3.9 years ago by DNAngel ▴ 250
2
votes
2
replies
963
views
Does spades/metaspades normally having missing nodes?
metaspades spades
3.9 years ago by DNAngel ▴ 250
3
votes
5
replies
1.6k
views
How to use lapply to extract taxonomic information in my species list?
R
3.9 years ago by DNAngel ▴ 250
0
votes
2
replies
761
views
How to get domain/kingdom name in a table of taxid in R tidyverse?
R
3.9 years ago by DNAngel ▴ 250
4
votes
3
replies
4.7k
views
kraken2 unclassified output does not work with paired reads?
Kraken2
updated 3.9 years ago by 102k • written 4.0 years ago by ▴ 250
1
vote
1
reply
1.6k
views
Best method to visualize metagenomic data besides krona?
metagenomics krona
updated 4.0 years ago by 3.9k • written 4.0 years ago by ▴ 250
3
votes
6
replies
4.3k
views
Bamtools stats and samtools flagstat produce different results and confusing my sambamba output.
sambamba bamtools samtools
4.0 years ago by DNAngel ▴ 250
0
votes
6
replies
3.5k
views
What do you do with the data processed after running metaspades/spades?
metaspades spades
updated 4.1 years ago by 3.9k • written 4.1 years ago by ▴ 250
0
votes
2
replies
1.3k
views
What to do with mapped reads after assembly?
Assembly annotation
4.3 years ago by DNAngel ▴ 250
0
votes
11
replies
2.0k
views
Error when trying to convert BAM file to FASTQ.
samtools bedtools
4.3 years ago by DNAngel ▴ 250
0
votes
6
replies
2.1k
views
FastQC Per sequence GC count always fails after trimmomatic?
fastqc trimmomatic
updated 4.3 years ago by 151k • written 4.3 years ago by ▴ 250
2
votes
13
replies
9.4k
views
How do you download the nt database for Kraken2?
Kraken2 nt
updated 4.3 years ago by 151k • written 4.3 years ago by ▴ 250
0
votes
6
replies
1.2k
views
Papers/posts on best practises for dealing with Illumina reads?
assembly trimmomatic bwa-mem
updated 4.3 years ago by 88k • written 4.3 years ago by ▴ 250
0
votes
2
replies
735
views
Determining if the number of significant results between two categories is significantly different?
statistics
4.5 years ago by DNAngel ▴ 250
0
votes
0
replies
639
views
How to know if it is missing a gene or assembly error?
BWA Assembly
updated 24 months ago by 45k • written 4.5 years ago by ▴ 250
0
votes
0
replies
667
views
PAML sample size question and variation in results
PAML
4.5 years ago by DNAngel ▴ 250
0
votes
0
replies
1.2k
views
Understanding PAML results between random-sites and clade model C.
PAML
4.6 years ago by DNAngel ▴ 250
2
votes
3
replies
2.2k
views
How to parallelize bwa mem for single-end data within a larger bash script?
bash bwa-mem gnu-parallel
updated 5.6 years ago by 166k • written 5.6 years ago by ▴ 250
2
votes
2
replies
2.7k
views
How do you extract longest transcript from fasta file using length and header IDs?
awk fasta
updated 5.6 years ago by 13k • written 5.6 years ago by ▴ 250
2
votes
1
reply
1.9k
views
How to loop over a directory to set each file as a variable?
bash
5.6 years ago by DNAngel ▴ 250
3
votes
7
replies
2.1k
views
Does Abyss work on single-end Illumina reads only?
Abyss
updated 5.6 years ago by 8.3k • written 5.6 years ago by ▴ 250
4
votes
6
replies
2.8k
views
How do you assemble contigs without using a reference genome?
assembly genome
updated 5.6 years ago by 35k • written 5.6 years ago by ▴ 250
1
vote
6
replies
2.8k
views
What do you do after obtaining sorted bam files?
bwa bam
updated 5.6 years ago by 14k • written 5.6 years ago by ▴ 250
0
votes
0
replies
924
views
How to obtain protein-coding sequences from assembled genome/exome dataset?
PAML bwa
5.6 years ago by DNAngel ▴ 250
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