Moderator: Philipp Bayer

gravatar for Philipp Bayer
Philipp Bayer6.7k
Reputation:
6,670
Status:
Trusted
Location:
Australia/Perth/UWA
Twitter:
PhilippBayer
Last seen:
1 day, 14 hours ago
Joined:
8 years, 2 months ago
Email:
p*********@googlemail.com

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

Posts by Philipp Bayer

<prev • 535 results • page 2 of 54 • next >
2
votes
2
answers
303
views
2
answers
Answer: A: Difficulties in Trinity installation
... I think if you install Trinity via conda or if you use the Singularity or Docker images provided you can circumvent this problem. What is the output of `which salmon`? That's what Trinity runs to check for your salmon installation. There's a chance that the salmon in /usr/bin/ isn't set to executab ...
written 6 months ago by Philipp Bayer6.7k
1
vote
1
answer
503
views
1
answers
Answer: A: Problems with SRA: curl: (9) Server denied you to change to the given directory
... I've had this recently too, where the official ftp didn't have a file the European or UK counterpart had. Sometimes the raw fastq works then: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/009/SRR1972739/SRR1972739_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR197/009/SRR1972739/SRR1972739_2 ...
written 8 months ago by Philipp Bayer6.7k
1
vote
0
answers
328
views
0
answers
Comment: C: publicly available data
... One avenue would be to check the SRA. Many, not all, BioProjects have a DOI of the paper they're associated with, so you could get the BioProject associated with the abstract without scanning the paper! ...
written 8 months ago by Philipp Bayer6.7k
2
votes
2
answers
1.0k
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 9 months ago by Philipp Bayer6.7k
6
votes
4
answers
426
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 10 months ago by Philipp Bayer6.7k
2
votes
1
answer
673
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 11 months ago by Philipp Bayer6.7k
1
vote
2
answers
464
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 11 months ago by Philipp Bayer6.7k
1
vote
2
answers
414
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 11 months ago by Philipp Bayer6.7k
0
votes
2
answers
464
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 11 months ago by Philipp Bayer6.7k
0
votes
1
answer
319
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 11 months ago by Philipp Bayer6.7k

Latest awards to Philipp Bayer

Appreciated 10 weeks ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Popular Question 5 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Scholar 5 months ago, created an answer that has been accepted. For A: Long reads Assembly Algorithms
Scholar 6 months ago, created an answer that has been accepted. For A: Long reads Assembly Algorithms
Appreciated 7 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Scholar 7 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Appreciated 8 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Appreciated 10 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Great Question 10 months ago, created a question with more than 5,000 views. For What Is One Book Every Bioinformatician Should Read?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Popular Question 11 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Scholar 12 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Appreciated 12 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Good Habit for Bioinformatics Analyst or Scientist
Scholar 12 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Librarian 13 months ago, created a post with more than 10 bookmarks. For What Is One Book Every Bioinformatician Should Read?
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?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 18 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: 620 users visited in the last hour