Moderator: Philipp Bayer

gravatar for Philipp Bayer
Philipp Bayer4.6k
Reputation:
4,560
Status:
Trusted
Location:
Australia/Perth/UWA
Twitter:
PhilippBayer
Last seen:
2 days, 7 hours ago
Joined:
5 years, 4 months ago
Email:
p*********@googlemail.com

Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org

Posts by Philipp Bayer

<prev • 371 results • page 1 of 38 • next >
2
votes
1
answer
185
views
1
answers
Answer: A: extracting data from bam file
... You could use bedtools genomecov aka genomeCoverageBed, slightly adjusted from the [manual][1]: samtools view -b chr3:123545-123965 | genomeCoverageBed -ibam stdin Add -bga to genomeCoverageBed if you want a different format which will also report bases with 0 coverage. [1]: http://bedtoo ...
written 13 days ago by Philipp Bayer4.6k
1
vote
1
answer
165
views
1
answers
Answer: A: SRA record can not be found!
... Looks like that submission was started but never finished: https://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=SRA112617 I've done that myself before, registered the accession so I had something for the paper, and then completely forgot about it. There's a chance the person you've contacted is as ...
written 15 days ago by Philipp Bayer4.6k
0
votes
3
answers
283
views
3
answers
Answer: A: Download SAM/BAM files from SRA takes ages!!!
... To download SRA files I always use ascp, [there's a manual here][1] It's ridiculously fast (the example command has a bandwith request of 100Mb/s, but I've used 400Mb/s before, depends on your local setup), then you can dump the fastq from the downloaded .sra file using the toolkit's `fastq-dump -- ...
written 29 days ago by Philipp Bayer4.6k
0
votes
1
answer
220
views
1
answers
Comment: C: Comparing Hi-c/dovetail, BioNano, and pacbio assemblies. Pick the best one?
... Yes, runBNG can scaffold your assembly fasta using the BioNano data, that would work! BTW there's also OMSim, which can simulate optical mapping data from your assembly; https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx293/3791407/OMSim-a-simulator-for-optical-map-data ...
written 4 weeks ago by Philipp Bayer4.6k
1
vote
1
answer
220
views
1
answers
Answer: A: Comparing Hi-c/dovetail, BioNano, and pacbio assemblies. Pick the best one?
... So there are a few papers which did what you're trying to do. In the goat genome paper they used both HiC and BioNano and found that HiC worked a bit better for them: http://www.nature.com/ng/journal/v49/n4/full/ng.3802.html They used Lachesis for HiC scaffolding with optimised parameters (somewher ...
written 5 weeks ago by Philipp Bayer4.6k
0
votes
6
answers
1.6k
views
6
answers
Comment: C: Stranger Things: unexpected limitations of popular tools
... Having uploaded data to the SRA I never had any phenotypes for that data in the first place (but this is, in my opinion, one of the biggest problems in bioinformatics - mountains of genomic data, hills of phenotype data) ...
written 5 weeks ago by Philipp Bayer4.6k
2
votes
6
answers
1.6k
views
6
answers
Answer: A: Stranger Things: unexpected limitations of popular tools
... SOAPaligner hasn't been updated since 2011 and still replaces N by G in alignments: https://www.biostars.org/p/101567/ But then again, I don't think people still use this aligner. OrthoMCL seems to have a bug when calculating paralogs where it keeps self-hits - PorthoMCL (reimplementation without ...
written 5 weeks ago by Philipp Bayer4.6k
0
votes
1
answer
159
views
1
answers
Comment: C: About the reads aligned 0 times (around 10%) in Bowtie2.
... In WGS, you always get 5-15% unaligning reads, so I usually don't bother too much there. Not sure about the numbers for ChIP-seq... ...
written 6 weeks ago by Philipp Bayer4.6k
4
votes
1
answer
159
views
1
answers
Answer: A: About the reads aligned 0 times (around 10%) in Bowtie2.
... These unaligning reads could be: - low quality reads (perhaps even containing Ns) - lab contamination from some other species (bacteria/fungi living on your species, human preparing your samples, sequencing machine wasn't cleaned properly and you get stuff from previous runs, that's what I've seen) ...
written 6 weeks ago by Philipp Bayer4.6k
0
votes
1
answer
190
views
1
answers
Answer: A: Trying to check if a query id appears in tabular blast output but not getting an
... A few things have happened here: 1) `blast_results` is just a file handler, there are no IDs stored. So when you check whether the record ID is in the blast results all you'll check with is this thing: ``. You'll have to store the blast results in a set or a list first, like blast_results = se ...
written 6 weeks ago by Philipp Bayer4.6k

Latest awards to Philipp Bayer

Scholar 20 days ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 4 weeks ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 6 weeks ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 12 weeks ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 3 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Scholar 4 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 5 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Epic Question 6 months ago, created a question with more than 10,000 views. For Best Way To Get Truly Unique Reads In Bowtie/Sam?
Scholar 6 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Appreciated 12 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Scholar 12 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1293 users visited in the last hour