User: colindaven

gravatar for colindaven
colindaven2.3k
Reputation:
2,260
Status:
Trusted
Location:
Hannover Medical School
Scholar ID:
Google Scholar Page
Last seen:
1 day, 6 hours ago
Joined:
4 years ago
Email:
c*********@hotmail.com

Staff Scientist Bioinformatics

Posts by colindaven

<prev • 361 results • page 1 of 37 • next >
0
votes
1
answer
127
views
1
answers
Comment: C: NCBI wants to remove quality scores from SRA
... Wow, the FASTQ from this with all set to 30 or 3 sounds ridiculously bad. It also would mark ALL long read data, both from Nanopore and Pacbio, as "reject" and give FASTQ out with quality values of 3. Why ? Because long read data is generally quality 8-15 at present. Great. I didn't know NCBI was ...
written 6 days ago by colindaven2.3k
0
votes
1
answer
70
views
1
answers
Answer: A: Assessing collapsed assembly ?
... You can try calling ORFs / genes in each and doing bidirectional blast to produce a CSV output, eg with proteinortho. https://www.biostars.org/p/359736/#359814 Alternatively, you could look at BUSCO which would be the more standard approach. ...
written 16 days ago by colindaven2.3k
0
votes
1
answer
74
views
1
answers
Answer: A: Filtering microbial variants
... You should be able to find a lot of information about this already on this site. What research have you done ? Also, I prefer multisample SNV calling, so you get a VCF with columns for each sample. This makes filtering a lot easier. Finally, I prefer to filter in Galaxy using eg SnpSift Filter and ...
written 16 days ago by colindaven2.3k
0
votes
0
answers
80
views
0
answers
Comment: C: Creating a bed file from a de novo fasta file
... Perhaps this would have helped with the names and lengths somewhat faster. Then adapt to BED format samtools faidx your.fasta cat your.fasta.fai ...
written 17 days ago by colindaven2.3k
1
vote
2
answers
85
views
2
answers
Answer: A: Removing UniVec sequences in Assembly
... We find adapters in genomes all the time which is terrible for metagenomics. This simple tool might help you to at least diagnose your problem and or replace the adapters with NNNs https://github.com/colindaven/blacklister Try additional adapter trimmers like -trimmomatic -fastp and after adapte ...
written 17 days ago by colindaven2.3k
0
votes
2
answers
605
views
2
answers
Answer: A: calculating abundance of metagenomes
... It's not really intended to answer your question, and you've probably solved this by now, but our pipeline can do the alignment and your intended normalization (including number of reads and genome length): https://github.com/MHH-RCUG/Wochenende Seeing as you have a custom output, you'll need to ...
written 17 days ago by colindaven2.3k
0
votes
73
answers
33k
views
73
answers
Comment: C: What Are The Most Common Stupid Mistakes In Bioinformatics?
... Yeah, the people who conceived of that were utterly brilliant usability specialists. ...
written 4 weeks ago by colindaven2.3k
1
vote
8
answers
2.4k
views
8
answers
Comment: C: RNASeq user experience with Novogene?
... ChIP-seq is very difficult. I'd do this over several cycles in house if possible first to test antibodies and workflow. At our core we do multiple iterations with the customer before we get good results, and then we go to a bigger sequencer for higher throughput. I would never recommend just sendi ...
written 8 weeks ago by colindaven2.3k
1
vote
1
answer
101
views
1
answers
Answer: A: How to replace the chromosome seq from new chromosome sequence in genome file
... Divide up the fasta using a script (there are various splitfasta style scripts out there in the world) then use the linux tool `cat` to concatenate the individual chromosomes including your new one back together. ...
written 8 weeks ago by colindaven2.3k
1
vote
1
answer
132
views
1
answers
Answer: A: Count total number of Homozygous/Heterozygous SNPs from VCF file
... Theres' a tool called **vt** (available via bioconda) which can do very nice summaries of vcf files. ...
written 8 weeks ago by colindaven2.3k

Latest awards to colindaven

Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Gene annotation pipeline for bacteria
Scholar 11 weeks ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Popular Question 4 months ago, created a question with more than 1,000 views. For Using the MinION MinKNOW software on Ubuntu 1604
Scholar 6 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 9 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Appreciated 10 months ago, created a post with more than 5 votes. For A: Gene annotation pipeline for bacteria
Popular Question 11 months ago, created a question with more than 1,000 views. For bbmap callvariants.sh on pacbio
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: is fortran still used in bioinformatics?
Scholar 12 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Appreciated 12 months ago, created a post with more than 5 votes. For A: Gene annotation pipeline for bacteria
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: is fortran still used in bioinformatics?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Guru 17 months ago, received more than 100 upvotes.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 17 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 18 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 987 users visited in the last hour