User: c.e.chong

gravatar for c.e.chong
c.e.chong20
Reputation:
20
Status:
New User
Location:
Last seen:
1 week, 4 days ago
Joined:
1 year, 4 months ago
Email:
c********@student.liverpool.ac.uk

Posts by c.e.chong

<prev • 27 results • page 1 of 3 • next >
0
votes
2
answers
5.0k
views
2
answers
Comment: C: How to generate Artemis ACT comparison file of multiple sequence alignment
... Thank you very much for your help! This makes so much sense now ...
written 3 months ago by c.e.chong20
0
votes
2
answers
5.0k
views
2
answers
Comment: C: How to generate Artemis ACT comparison file of multiple sequence alignment
... Hi all, I tried to use this script for to compare two fasta files that contain around 60 contigs each. When I input this into ACT I only seem to get similarity information for the first contig? Both fasta files are the same bacterial species so expected to be pretty similar. Do you have any advi ...
written 3 months ago by c.e.chong20
0
votes
0
answers
187
views
0
answers
Comment: C: Bowtie database of all bacterial and fungal complete genomes
... Thank you for your reply! I have considered getting representatives for broad classes. My plan was to use CD-HIT to remove redundancy once I had downloaded all of the bacterial and fungal complete genomes, do you think this is the best method? I have used Kraken2 but I want to access the bam fil ...
written 6 months ago by c.e.chong20
1
vote
0
answers
187
views
0
answers
Bowtie database of all bacterial and fungal complete genomes
... Hi all, I would like to create a database of all the bacterial and fungal complete genomes in the RefSeq database to map all of my Metagenome samples to it. Does anyone know if this is possible? The manual states that you have to input a comma separated list of fasta files to build the database, ...
bowtie2 metagenomics mapping shotgun written 7 months ago by c.e.chong20
0
votes
1
answer
701
views
1
answers
Comment: C: Kraken2 to Phyloseq
... Thank you for your reply, is there a preferred method for generating a table of the number of reads mapped to each contig from the bam file? Is this the same as calculating coverage? Also is DeSeq recommended to find taxonomic differences between samples/groups of samples? Or more the genes within ...
written 7 months ago by c.e.chong20
0
votes
1
answer
701
views
1
answers
Comment: C: Kraken2 to Phyloseq
... I have previously mapped my reads to databases made from the contigs of each sample when using anvio to bin my samples. Would these bam files contain the sufficient information to do the comparisons? To use kraken to find out what the differential contigs are should I input the concoct contig bins I ...
written 7 months ago by c.e.chong20
5
votes
1
answer
701
views
1
answer
Kraken2 to Phyloseq
... Hi all, I am quite new to Metagenomics and how to statistically analyse my data. I have run kraken2 to taxonomically profile my assembled metagenomics samples. I have three different disease state groups and I would like to see if there are any statistical differences between them. I decided to ...
R kraken shotgun metagenomics statistics written 7 months ago by c.e.chong20 • updated 7 months ago by Asaf6.8k
0
votes
1
answer
559
views
1
answers
Comment: C: Java error message when using BBDuk
... That worked! Such a simple fix!! Thank you very much! ...
written 10 months ago by c.e.chong20
0
votes
1
answer
559
views
1
answers
Comment: C: Java error message when using BBDuk
... That worked! Such a simple fix!! Thank you very much! ...
written 10 months ago by c.e.chong20
0
votes
1
answer
559
views
1
answers
Comment: C: Java error message when using BBDuk
... Yes, my files are already trimmed for adapters I am now doing a quality trim. I tried with the lower number of RAM and threads and got this error: Exception in thread "main" java.lang.NullPointerException at shared.Parser.parseTrim(Parser.java:333) at jgi.BBDuk.(BBDuk.java:176) ...
written 10 months ago by c.e.chong20 • updated 10 months ago by genomax76k

Latest awards to c.e.chong

Popular Question 6 months ago, created a question with more than 1,000 views. For bbmap split paired-end reads back into separated fastq files?
Popular Question 6 months ago, created a question with more than 1,000 views. For bbmap split paired-end reads back into separated fastq files?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1035 users visited in the last hour