User: David

gravatar for David
David50
Reputation:
50
Status:
Trusted
Location:
Last seen:
1 month, 2 weeks ago
Joined:
1 year, 6 months ago
Email:
v******@gmail.com

Posts by David

<prev • 40 results • page 1 of 4 • next >
0
votes
0
answers
123
views
0
answers
Simulated overlapping paired end reads for 16S
... Hi, I have a fasta files with 16S sequences from 20 different species. I would like to generate paired end reads (overlapping). I was trying to use the following command form the bbmap package: > randomreads.sh ref=20_species_16S.fasta out=read.R1.fq.gz out2=read.R2.fq.gz paired reads=1000 ...
bbmap written 6 weeks ago by David50
0
votes
0
answers
115
views
0
answers
Get non redundant from Bacteria Archaea Fungi
... Hello, I have downloaded Non redundant protein database from NCBI. The thing is that i´m only interested in Bacteria, Archaea , Fungi . Is there a quick way to filter this file Refseq is not suitable for me because some sequences are not yet in there. Is there a quick way of doing this ?? Thanks ...
ncbi rna-seq written 7 weeks ago by David50
0
votes
2
answers
143
views
2
answers
Answer: A: Lowest common ancestor
... OOpps, Was too fast writing my question. I have a fasta file that i have blasted (using diamond -m8) to Non redundant proteins. I would like to parse the output and find the LCA from the output. Is there any tool outhere (such as lcamapper.sh from MEgan) ?? thanks, ...
written 7 weeks ago by David50
1
vote
2
answers
143
views
2
answers
Lowest common ancestor
... Hello, Is there any tool available to run a lowest common ancestor from a fasta file ??? I have found MEGAN6 but i'm looking for an independent tool if it exists ?? Thanks, david ...
lca taxonomy written 7 weeks ago by David50
0
votes
1
answer
174
views
1
answers
Comment: C: fastqc gc-content peak and adapter content
... Ok great. Yes I will start cleaning data. thanks ...
written 9 weeks ago by David50
2
votes
1
answer
174
views
1
answer
fastqc gc-content peak and adapter content
... Hi, I have the following fastqc profile and i´m just trying to understand what´s wrong with blue line. This is a human microRNA rna seq experiment (1x50bp) from human blood extracted microRNAs. In adapter content it starts around 18 (y axis) (small RNA 3´adapter). Why is that ?? Too much adapter ? ...
fastqc written 9 weeks ago by David50
0
votes
1
answer
300
views
1
answers
Comment: A: Normalize bedtools gene coverage by total number of reads
... Hi, Couldn´t manage to get genes coverage using coverageCounts. It returns binary files. How would you get the gene coverage as numeric ? ...
written 12 weeks ago by David50
0
votes
1
answer
300
views
1
answers
Comment: A: Normalize bedtools gene coverage by total number of reads
... Ok found it coverageCounts. Great I´ll normalize with Deseq2 , thanks ...
written 12 weeks ago by David50
0
votes
1
answer
300
views
1
answers
Comment: A: Normalize bedtools gene coverage by total number of reads
... Thanks for your comments Carlo, Can you generate coverage using FeatureCounts from bam files ?? ...
written 12 weeks ago by David50
0
votes
0
answers
222
views
0
answers
Comment: C: Normalization methods for metagenomics WGS data (not 16S data)
... I have a reads count table corersponding to a metagenomics experiment. I have cleared the reads (removed contaminants and filtered low quality reads). I have assigned taxonomy to the reads and build a table. Now i have a table (each column being a sample and each row being a taxa). I want to compar ...
written 3 months ago by David50

Latest awards to David

Student 12 weeks ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)
Student 4 months ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 455 users visited in the last hour