Moderator: Philipp Bayer

gravatar for Philipp Bayer
Philipp Bayer6.6k
Reputation:
6,590
Status:
Trusted
Location:
Australia/Perth/UWA
Twitter:
PhilippBayer
Last seen:
22 hours ago
Joined:
7 years, 10 months ago
Email:
p*********@googlemail.com

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

Posts by Philipp Bayer

<prev • 532 results • page 2 of 54 • next >
2
votes
2
answers
974
views
2
answers
Answer: A: SSD or HHD for genome analisys
... Interestingly, there's a whole paper about this! https://academic.oup.com/bib/article/17/4/713/2240499/ It looks like some programs sped up significantly, others had no improvement. Personally I'd rather go for space than for speed (so the 2x2TB HDD), but I work with massive plant genomes, I don't ...
written 4 months ago by Philipp Bayer6.6k
6
votes
4
answers
381
views
4
answers
Answer: A: Putting R codes on MS word document
... You can write your whole analysis in Markdown including your code blocks, and then render it into Word and back using redoc: https://github.com/noamross/redoc ...
written 5 months ago by Philipp Bayer6.6k
2
votes
1
answer
453
views
1
answers
Answer: A: Maker Annotation pipeline Output error
... Have you run the MAKER scripts `fasta_merge` to create the protein/transcript fasta files and `gff3_merge` to create the final gff file? ...
written 6 months ago by Philipp Bayer6.6k
1
vote
2
answers
380
views
2
answers
Answer: A: Annotation lifting to a different organism
... I *may* have a solution - I've had a similar error recently with an annotation that had many non-gene entries, i.e., snoRNAs, rRNAs, tRNAs etc. and those kept on causing problems in flo. After removing them all with this simple Python 3 script it worked fine (YMMV) bad_ones = set(['nCRNA','snoRNA' ...
written 6 months ago by Philipp Bayer6.6k
1
vote
2
answers
294
views
2
answers
Answer: A: A software tool for gene copy number and loss detection
... I've made good experiences with cn.MOPS: https://bioconductor.org/packages/release/bioc/html/cn.mops.html (which overlap quite a bit with a simplistic SGSGeneloss approach based on mosdepth and some scripting :) ) Hecaton is new and looking at the paper, it's quite exciting, but it's tailored at p ...
written 6 months ago by Philipp Bayer6.6k
0
votes
2
answers
380
views
2
answers
Comment: C: Annotation lifting to a different organism
... What does the output of /QRISdata/Q0231/apps/flo/gff_recover.rb run/TAIR10_GFF3_genes-fix1/lifted.gff3 | head say? ...
written 6 months ago by Philipp Bayer6.6k
0
votes
1
answer
232
views
1
answers
Answer: A: "ERROR:...Base position exceeds Integer.MAX_VALUE" using Refined IBD with map fi
... Integer.MAX_VALUE is a Java-internal hard-coded value, googling around it should be 2,147,483,647 on most systems - do you have base positions larger than that? ...
written 6 months ago by Philipp Bayer6.6k
0
votes
1
answer
246
views
1
answers
Answer: A: find orthology genes
... Looking at the hamstr code at https://github.com/BIONF/HaMStR/blob/master/bin/hamstr.pl, this error you're seeing: `"checking for presence of the hmm files:`, prints a few more lines to the log-file, NOT to the standard out: in case the hmmset is broken it writes this to the log file: push @l ...
written 7 months ago by Philipp Bayer6.6k
0
votes
1
answer
256
views
1
answers
Answer: A: Augustus output (GFF file) to Anvi`o
... I've made good experiences with this script: https://github.com/jorvis/biocode/blob/master/gff/convert_augustus_to_gff3.py when downstream software wasn't liking the AUGUSTUS gff3 (you'll have to run `pip install biocode` first) ...
written 7 months ago by Philipp Bayer6.6k
0
votes
1
answer
239
views
1
answers
Answer: A: Bias in GO enrichment analysis for non-model organsim?
... Yes, this is an important point that is often ignored in plant genomics papers! Here's a paper discussing GO database bias, with a bit on the bias imported by unannotated genes, but this is all in human: https://www.nature.com/articles/s41598-018-23395-2 The other problem is that most of your genes ...
written 7 months ago by Philipp Bayer6.6k

Latest awards to Philipp Bayer

Popular Question 23 days ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Long reads Assembly Algorithms
Scholar 6 weeks ago, created an answer that has been accepted. For A: Long reads Assembly Algorithms
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Scholar 11 weeks ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Appreciated 4 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Appreciated 5 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Great Question 5 months ago, created a question with more than 5,000 views. For What Is One Book Every Bioinformatician Should Read?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Popular Question 7 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Scholar 7 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Appreciated 7 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Good Habit for Bioinformatics Analyst or Scientist
Scholar 8 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Librarian 8 months ago, created a post with more than 10 bookmarks. For What Is One Book Every Bioinformatician Should Read?
Popular Question 9 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 13 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Popular Question 14 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1166 users visited in the last hour