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1
vote
3
replies
346
views
Why is DESeq2 normalization making my top feature have identical values across samples?
DESEQ2 WGCNA
25 days ago by DNAngel ▴ 250
0
votes
0
replies
129
views
Should I keep taxa that have 0 counts when calculating alpha diversity?
Shannon-Weiner
4 weeks ago by DNAngel ▴ 250
0
votes
5
replies
861
views
Samtools unmapped reads
samtools
14 months ago by DNAngel ▴ 250
0
votes
3
replies
1.0k
views
Samtools mapped and unmapped flags, what is the difference between the flags?
samtools
15 months ago by DNAngel ▴ 250
2
votes
2
replies
600
views
How do you get functional/biological role of motifs?
JASPAR
updated 15 months ago by 4.6k • written 15 months ago by ▴ 250
2
votes
8
replies
1.2k
views
How to get names and class information from a list of target IDs from the JASPAR database?
JASPAR
updated 15 months ago by 82k • written 15 months ago by ▴ 250
3
votes
3
replies
692
views
Program to detect cis-regulatory modules for a non model species?
factors transcription
17 months ago by DNAngel ▴ 250
4
votes
3
replies
789
views
How do you find transcription factors in a newly sequenced genome?
interproscan factors transcription
updated 18 months ago by ▴ 20 • written 18 months ago by ▴ 250
7
votes
8
replies
1.0k
views
How do you obtain a list of transcription factors from a genome?
transcription-factor
updated 13 months ago by 43k • written 19 months ago by ▴ 250
0
votes
6
replies
1.9k
views
Confused about which database to use - nt or nr?
blast
updated 19 months ago by 11k • written 19 months ago by ▴ 250
0
votes
2
replies
688
views
What happened to the SparCC github repository?
sparcc
updated 2.0 years ago by ★ 2.0k • written 2.0 years ago by ▴ 250
2
votes
8
replies
3.3k
views
Why does Kraken2 not produce taxon percentages with --report flag?
kraken2
updated 2.4 years ago by ▴ 100 • written 3.0 years ago by ▴ 250
0
votes
0
replies
616
views
Can I use DESeq2 to analyze my abundance dataset, which also happens to have a lot of zeros?
deseq2
2.6 years ago by DNAngel ▴ 250
2
votes
4
replies
1.3k
views
WGCNA, what does it mean if no hub genes are identified?
WGCNA
2.6 years ago by DNAngel ▴ 250
1
vote
0
replies
590
views
R package for determining best model transformation for a dataset?
R
2.7 years ago by DNAngel ▴ 250
11
votes
15
replies
3.4k
views
Output of samtools view, what does the third column actually represent?
samtools
updated 2.7 years ago by 19k • written 2.7 years ago by ▴ 250
0
votes
0
replies
572
views
How to find out how many reads were used in contig assembly in metaSPADES?
metaspades
2.7 years ago by DNAngel ▴ 250
1
vote
1
reply
1.6k
views
How do you interpret Tukey's significance when there is no group clustering alone?
Tukey
2.7 years ago by DNAngel ▴ 250
1
vote
1
reply
1.3k
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 2.7 years ago by 142k • written 2.7 years ago by ▴ 250
0
votes
0
replies
530
views
R vegdist does not compute distances for all my sites
vegan vegdist R
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 250
3
votes
1
reply
1.9k
views
What is the recommended contig length to filter?
metaspades
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 250
2
votes
6
replies
1.1k
views
Is there a different names.dmp file in the taxonomy name/id browser?
ncbi
updated 2.8 years ago by 142k • written 2.8 years ago by ▴ 250
1
vote
11
replies
1.8k
views
Blast 2.11 not blasting all sequences in a file?
blast
2.9 years ago by DNAngel ▴ 250
7
votes
12
replies
1.7k
views
7 follow
Why do I lose sequences when converting my bam files into fastq?
fastq bam bamToFastq
updated 2.9 years ago by 14k • written 2.9 years ago by ▴ 250
0
votes
0
replies
681
views
Confused about sambamba syntax for unmapped and mapped
sambamba
2.9 years ago by DNAngel ▴ 250
2
votes
2
replies
703
views
Does spades/metaspades normally having missing nodes?
metaspades spades
2.9 years ago by DNAngel ▴ 250
3
votes
5
replies
1.2k
views
How to use lapply to extract taxonomic information in my species list?
R
2.9 years ago by DNAngel ▴ 250
0
votes
2
replies
609
views
How to get domain/kingdom name in a table of taxid in R tidyverse?
R
2.9 years ago by DNAngel ▴ 250
2
votes
3
replies
3.2k
views
kraken2 unclassified output does not work with paired reads?
Kraken2
updated 2.9 years ago by 100k • written 2.9 years ago by ▴ 250
1
vote
1
reply
1.3k
views
Best method to visualize metagenomic data besides krona?
metagenomics krona
updated 3.0 years ago by 3.6k • written 3.0 years ago by ▴ 250
3
votes
6
replies
2.9k
views
Bamtools stats and samtools flagstat produce different results and confusing my sambamba output.
sambamba bamtools samtools
2.9 years ago by DNAngel ▴ 250
0
votes
6
replies
2.5k
views
What do you do with the data processed after running metaspades/spades?
metaspades spades
updated 3.0 years ago by 3.6k • written 3.0 years ago by ▴ 250
0
votes
2
replies
871
views
What to do with mapped reads after assembly?
Assembly annotation
3.2 years ago by DNAngel ▴ 250
0
votes
11
replies
1.4k
views
Error when trying to convert BAM file to FASTQ.
samtools bedtools
3.3 years ago by DNAngel ▴ 250
0
votes
6
replies
1.7k
views
FastQC Per sequence GC count always fails after trimmomatic?
fastqc trimmomatic
updated 3.3 years ago by 142k • written 3.3 years ago by ▴ 250
2
votes
13
replies
7.1k
views
How do you download the nt database for Kraken2?
Kraken2 nt
updated 3.3 years ago by 142k • written 3.3 years ago by ▴ 250
0
votes
6
replies
914
views
Papers/posts on best practises for dealing with Illumina reads?
assembly trimmomatic bwa-mem
updated 3.3 years ago by 82k • written 3.3 years ago by ▴ 250
0
votes
2
replies
584
views
Determining if the number of significant results between two categories is significantly different?
statistics
3.5 years ago by DNAngel ▴ 250
0
votes
0
replies
489
views
How to know if it is missing a gene or assembly error?
BWA Assembly
updated 11 months ago by 43k • written 3.5 years ago by ▴ 250
0
votes
0
replies
530
views
PAML sample size question and variation in results
PAML
3.5 years ago by DNAngel ▴ 250
0
votes
0
replies
992
views
Understanding PAML results between random-sites and clade model C.
PAML
3.6 years ago by DNAngel ▴ 250
2
votes
3
replies
1.8k
views
How to parallelize bwa mem for single-end data within a larger bash script?
bash bwa-mem gnu-parallel
updated 4.5 years ago by 161k • written 4.5 years ago by ▴ 250
2
votes
2
replies
2.2k
views
How do you extract longest transcript from fasta file using length and header IDs?
awk fasta
updated 4.6 years ago by 13k • written 4.6 years ago by ▴ 250
2
votes
1
reply
1.8k
views
How to loop over a directory to set each file as a variable?
bash
4.6 years ago by DNAngel ▴ 250
3
votes
7
replies
1.5k
views
Does Abyss work on single-end Illumina reads only?
Abyss
updated 4.6 years ago by 8.2k • written 4.6 years ago by ▴ 250
4
votes
6
replies
2.1k
views
How do you assemble contigs without using a reference genome?
assembly genome
updated 4.6 years ago by 35k • written 4.6 years ago by ▴ 250
1
vote
6
replies
2.2k
views
What do you do after obtaining sorted bam files?
bwa bam
updated 4.6 years ago by 14k • written 4.6 years ago by ▴ 250
0
votes
0
replies
779
views
How to obtain protein-coding sequences from assembled genome/exome dataset?
PAML bwa
4.6 years ago by DNAngel ▴ 250
0
votes
0
replies
683
views
How to test evolutionary rates for each species in a gene alignment?
evolutionary rate R
4.7 years ago by DNAngel ▴ 250
0
votes
0
replies
1.0k
views
R package to calculate ancestral state characters using maximum parsimony?
R maximum parsimony ancestral states
4.9 years ago by DNAngel ▴ 250
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