User: colindaven

gravatar for colindaven
colindaven490
Reputation:
490
Status:
Trusted
Location:
Last seen:
23 hours ago
Joined:
1 year, 7 months ago
Email:
c*********@hotmail.com

Posts by colindaven

<prev • 107 results • page 1 of 11 • next >
2
votes
1
answer
107
views
1
answers
Answer: A: SNP Positioning on a Gene
... Have a look at snpEff or Ensembl VEP ...
written 7 days ago by colindaven490
2
votes
1
answer
158
views
1
answers
Answer: A: Unable to install bwa-0.7.17 on ubuntu 10.06 virtualbox machine.
... I would recommend bioconda for this. It really makes installing software a piece of cake, and is itself very easy to install. Give it a go! ...
written 6 weeks ago by colindaven490
0
votes
1
answer
186
views
1
answers
Answer: A: Is there a way to separate highly similar strains from metatranscriptomic data u
... First, why use HISAT2 ? Are these prokaryotes or pico-eukaryotes ? If prokaryotes I would not use a spliced aligner. Always align to all genomes at once, including contaminants (human?). Maybe you can find a draft assembly of the new genome as well. I once created a file like this, which was usef ...
written 7 weeks ago by colindaven490
1
vote
3
answers
304
views
3
answers
Answer: A: finding contigs present in one assembly but missing from another
... I would use a bidirectional blastn program for this. You can predict ORFs and use blastx/blastp if looking at gene content (which might be easier for setting useful e-value cutoffs) or just use blastn. Long contigs will almost always tend to have hits with blastn though. I have used proteinortho fo ...
written 7 weeks ago by colindaven490
1
vote
0
answers
183
views
0
answers
Comment: A: Mikado prepare error
... Why not ask in a github issue, the authors are friendly and quick to reply! ...
written 7 weeks ago by colindaven490
1
vote
4
answers
256
views
4
answers
Answer: A: denovo assembly combining multiple data sets
... Soapdenovo2 would be useful for this as it allows simple use of different libraries (if you want to do this). I don't think the Ion Torrent reads are going to help at all though, since they are a shorter read length and not paired end. To my knowledge they also contain a lot of indel errors, which ...
written 7 weeks ago by colindaven490
0
votes
1
answer
200
views
1
answers
Answer: A: Canu Assembly: BAM input file?
... You can use a tool like bamtofastq to extract reads and pass these in. I'm not sure if BAM is an allowed input these days, but I don't think so. bamtofastq filename=m54055_170517_074454.subreads.bam > 1K2_dig_subreads.fastq You can find this in biobambam, available via bioconda. ...
written 9 weeks ago by colindaven490
0
votes
1
answer
273
views
1
answers
Answer: A: Metagenomic analysis workflow
... Combining the samples sounds like a really, really bad idea. You might get better assembly stats but on an assembly of messed up chimeras. This is not going to help you. Also try a read based binning method (as opposed to contigs). You are likely to get more accurate semiquantitative abundance valu ...
written 9 weeks ago by colindaven490
0
votes
1
answer
253
views
1
answers
Answer: A: bash: tophat: command not found
... Why not have a look at a modern pipeline such as NGI-RNA-seq https://github.com/SciLifeLab/NGI-RNAseq ? This will get you going a lot quicker. Also, I'd recommend using Linux over Mac since most software is better supported there. ...
written 9 weeks ago by colindaven490
0
votes
0
answers
241
views
0
answers
Comment: C: PacBio reads polishing
... What are you trying to do ? Assembling what? If just going for a general bacterial assembly, canu just takes one command to polish and assemble. If you want to follow the DAZZLER approach I think you'd best start with FALCON https://github.com/PacificBiosciences/FALCON ...
written 10 weeks ago by colindaven490

Latest awards to colindaven

Voter 6 weeks ago, voted more than 100 times.
Centurion 9 weeks ago, created 100 posts.
Scholar 3 months ago, created an answer that has been accepted. 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
Scholar 5 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Teacher 8 months ago, created an answer with at least 3 up-votes. 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
Scholar 12 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 14 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Supporter 16 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1209 users visited in the last hour