User: colindaven

gravatar for colindaven
colindaven640
Reputation:
640
Status:
Trusted
Location:
Hannover Medical School
Last seen:
15 hours ago
Joined:
1 year, 10 months ago
Email:
c*********@hotmail.com

Posts by colindaven

<prev • 128 results • page 1 of 13 • next >
0
votes
1
answer
71
views
1
answers
Answer: A: Decision on no. and type of libraries to be generated for plant genome assembly
... 600mb is not too huge these days. I would go for Pacbio 40-50X coverage depending on your budget. The longest reads are really important. Secondly, you are going to **need** an Illumina paired end library to correct the short errors in the Pacbio assembly. Coverage 30X. I would really avoid a true ...
written 1 day ago by colindaven640
1
vote
2
answers
118
views
2
answers
Answer: A: Phased Genome, Want reads From Both Alleles
... This whole project is very demanding. I would recommend looking at Phaser https://github.com/secastel/phaser However, I spent a long time working on this, and got very little out. Nanopore is a better option for getting phased alleles in my opinion. Good luck. ...
written 20 days ago by colindaven640
1
vote
1
answer
187
views
1
answers
Comment: C: How to do correlation analyses between RNAseq and ChIPseq library?
... Good point, often zeros are (optionally) excluded by the tool which then creates a matrix and performs the correlation, eg. deeptools. ...
written 24 days ago by colindaven640
1
vote
1
answer
150
views
1
answers
Comment: C: Pearson correlation between chIP-seq replicates is very poor- am I doing somethi
... In that case, if multibamsummary can't handle groups of multiple bam files, just combine the IP and input bams into IP.bam and input.bam, then run again. I wouldn't recommend this, replicates are there for a very very good reason. The docs on multibamsummary are pretty clear multiBamSummary co ...
written 25 days ago by colindaven640
1
vote
1
answer
88
views
1
answers
Answer: A: Platanus only use single thread
... You need to have a lot of patience for genome assembly. Most tools have steps where only one thread is used, ie. for initial IO or steps which have not yet been parallelized. ...
written 25 days ago by colindaven640
0
votes
1
answer
150
views
1
answers
Comment: C: Pearson correlation between chIP-seq replicates is very poor- am I doing somethi
... So which steps are you doing exactly ? I just follow the Galaxy training ChIP-seq tutorial which is rather nice : http://galaxyproject.github.io/training-material/topics/chip-seq/tutorials/tal1-binding-site-identification/tutorial.html So far results have been very sensible. However, it could be yo ...
written 26 days ago by colindaven640
0
votes
1
answer
471
views
1
answers
Answer: A: Difference in number of peaks called
... Shouldn't you be calling each against the Input (same chip-seq process, but not applying the antibody) for these data, not against WT or control ? Have you looked at the plotfingerprints method from Deeptools - in Galaxy ? ...
written 4 weeks ago by colindaven640
2
votes
1
answer
136
views
1
answers
Answer: A: genomic analysis workflow for plants
... Single ended FASTQ files only are going to work very badly for a plant genome which is likely large and repetitive. If a reference genome is available I would do alignments instead. If you have to assemble contigs, you might try Soapdenovo2, but I would not expect much. Also Ion Torrent has lots of ...
written 4 weeks ago by colindaven640
0
votes
3
answers
158
views
3
answers
Answer: A: Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads
... Medusa may work https://github.com/combogenomics/medusa ...
written 4 weeks ago by colindaven640
0
votes
1
answer
131
views
1
answers
Answer: A: PacBio amplicon sequencing
... What I do with long read amplicon data: The high coverage and high error rates are the problem - downsample (reduce) the number of reads so you can actually view it in a genome browser as you might have 10000x + coverage, samtools view -h -s 0.01 x_100k.fa_s.bam > x_100k.fa_s_one_percent.bam - ...
written 4 weeks ago by colindaven640

Latest awards to colindaven

Voter 4 months ago, voted more than 100 times.
Centurion 5 months ago, created 100 posts.
Scholar 6 months ago, created an answer that has been accepted. For A: Gene annotation pipeline for bacteria
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Scholar 7 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Gene annotation pipeline for bacteria
Appreciated 15 months ago, created a post with more than 5 votes. For A: Gene annotation pipeline for bacteria
Scholar 15 months ago, created an answer that has been accepted. For A: Best way to compare two samples in a VCF file
Teacher 16 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: Best way to compare two samples in a VCF file
Supporter 19 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: 1020 users visited in the last hour