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questions
1
vote
3
replies
302
views
Why is DESeq2 normalization making my top feature have identical values across samples?
DESEQ2
WGCNA
8 days ago by
DNAngel
▴ 250
0
votes
0
replies
113
views
Should I keep taxa that have 0 counts when calculating alpha diversity?
Shannon-Weiner
15 days ago by
DNAngel
▴ 250
0
votes
5
replies
832
views
Samtools unmapped reads
samtools
14 months ago by
DNAngel
▴ 250
0
votes
3
replies
977
views
Samtools mapped and unmapped flags, what is the difference between the flags?
samtools
14 months ago by
DNAngel
▴ 250
2
votes
2
replies
583
views
How do you get functional/biological role of motifs?
JASPAR
updated 15 months ago by
Matthias Zepper
4.5k • written 15 months ago by
DNAngel
▴ 250
2
votes
8
replies
1.1k
views
How to get names and class information from a list of target IDs from the JASPAR database?
JASPAR
updated 15 months ago by
ATpoint
81k • written 15 months ago by
DNAngel
▴ 250
3
votes
3
replies
676
views
Program to detect cis-regulatory modules for a non model species?
factors
transcription
17 months ago by
DNAngel
▴ 250
4
votes
3
replies
765
views
How do you find transcription factors in a newly sequenced genome?
interproscan
factors
transcription
updated 18 months ago by
xmLiu
▴ 20 • written 18 months ago by
DNAngel
▴ 250
7
votes
8
replies
975
views
How do you obtain a list of transcription factors from a genome?
transcription-factor
updated 13 months ago by
Ram
43k • written 18 months ago by
DNAngel
▴ 250
0
votes
6
replies
1.8k
views
Confused about which database to use - nt or nr?
blast
updated 18 months ago by
5heikki
11k • written 18 months ago by
DNAngel
▴ 250
0
votes
2
replies
666
views
What happened to the SparCC github repository?
sparcc
updated 24 months ago by
Wayne
★ 1.9k • written 24 months ago by
DNAngel
▴ 250
2
votes
8
replies
3.3k
views
Why does Kraken2 not produce taxon percentages with --report flag?
kraken2
updated 2.3 years ago by
Giulia.cosenza
▴ 100 • written 3.0 years ago by
DNAngel
▴ 250
0
votes
0
replies
608
views
Can I use DESeq2 to analyze my abundance dataset, which also happens to have a lot of zeros?
deseq2
2.5 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
582
views
R package for determining best model transformation for a dataset?
R
2.6 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 2.6 years ago by
i.sudbery
19k • written 2.6 years ago by
DNAngel
▴ 250
0
votes
0
replies
564
views
How to find out how many reads were used in contig assembly in metaSPADES?
metaspades
2.6 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
2.6 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
GenoMax
141k • written 2.7 years ago by
DNAngel
▴ 250
0
votes
0
replies
523
views
R vegdist does not compute distances for all my sites
vegan
vegdist
R
updated 2.7 years ago by
Ram
43k • written 2.7 years ago by
DNAngel
▴ 250
3
votes
1
reply
1.9k
views
What is the recommended contig length to filter?
metaspades
updated 2.7 years ago by
Mensur Dlakic
★ 27k • written 2.7 years ago by
DNAngel
▴ 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
GenoMax
141k • written 2.8 years ago by
DNAngel
▴ 250
1
vote
11
replies
1.8k
views
Blast 2.11 not blasting all sequences in a file?
blast
2.8 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
swbarnes2
14k • written 2.9 years ago by
DNAngel
▴ 250
0
votes
0
replies
671
views
Confused about sambamba syntax for unmapped and mapped
sambamba
2.9 years ago by
DNAngel
▴ 250
2
votes
2
replies
687
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
601
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
Istvan Albert
100k • written 2.9 years ago by
DNAngel
▴ 250
1
vote
1
reply
1.3k
views
Best method to visualize metagenomic data besides krona?
metagenomics
krona
updated 2.9 years ago by
andres.firrincieli
3.6k • written 2.9 years ago by
DNAngel
▴ 250
3
votes
6
replies
2.8k
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
andres.firrincieli
3.6k • written 3.0 years ago by
DNAngel
▴ 250
0
votes
2
replies
855
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
3.2 years ago by
DNAngel
▴ 250
0
votes
6
replies
1.7k
views
FastQC Per sequence GC count always fails after trimmomatic?
fastqc
trimmomatic
updated 3.2 years ago by
GenoMax
141k • written 3.2 years ago by
DNAngel
▴ 250
2
votes
13
replies
7.0k
views
How do you download the nt database for Kraken2?
Kraken2
nt
updated 3.2 years ago by
GenoMax
141k • written 3.2 years ago by
DNAngel
▴ 250
0
votes
6
replies
897
views
Papers/posts on best practises for dealing with Illumina reads?
assembly
trimmomatic
bwa-mem
updated 3.2 years ago by
ATpoint
81k • written 3.2 years ago by
DNAngel
▴ 250
0
votes
2
replies
578
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
479
views
How to know if it is missing a gene or assembly error?
BWA
Assembly
updated 11 months ago by
Ram
43k • written 3.5 years ago by
DNAngel
▴ 250
0
votes
0
replies
527
views
PAML sample size question and variation in results
PAML
3.5 years ago by
DNAngel
▴ 250
0
votes
0
replies
984
views
Understanding PAML results between random-sites and clade model C.
PAML
3.5 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
Pierre Lindenbaum
161k • written 4.5 years ago by
DNAngel
▴ 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 4.5 years ago by
JC
13k • written 4.5 years ago by
DNAngel
▴ 250
2
votes
1
reply
1.8k
views
How to loop over a directory to set each file as a variable?
bash
4.5 years ago by
DNAngel
▴ 250
3
votes
7
replies
1.5k
views
Does Abyss work on single-end Illumina reads only?
Abyss
updated 4.5 years ago by
Charles Warden
8.2k • written 4.5 years ago by
DNAngel
▴ 250
4
votes
6
replies
2.1k
views
How do you assemble contigs without using a reference genome?
assembly
genome
updated 4.5 years ago by
h.mon
35k • written 4.5 years ago by
DNAngel
▴ 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
swbarnes2
14k • written 4.6 years ago by
DNAngel
▴ 250
0
votes
0
replies
771
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
676
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
993
views
R package to calculate ancestral state characters using maximum parsimony?
R
maximum parsimony
ancestral states
4.9 years ago by
DNAngel
▴ 250
67 results • Page
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