Moderator: Philipp Bayer

gravatar for Philipp Bayer
Philipp Bayer5.8k
Reputation:
5,770
Status:
Trusted
Location:
Australia/Perth/UWA
Twitter:
PhilippBayer
Last seen:
2 days, 5 hours ago
Joined:
6 years, 7 months ago
Email:
p*********@googlemail.com

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

Posts by Philipp Bayer

<prev • 467 results • page 2 of 47 • next >
1
vote
1
answer
166
views
1
answers
Answer: A: Cuffmerge and cuffdiff error
... What's in your assemblies.txt? I have a hunch that your original RNASeq alignments never finished, as all of your software complains about missing end-of-file markers. You can check your input bam files using samtools view your_alignment.bam > /dev/null if it still complains about EOF miss ...
written 7 weeks ago by Philipp Bayer5.8k
0
votes
1
answer
163
views
1
answers
Answer: A: is there a faster way to download large sequencing data from NCBI?
... I've made very good experiences with ascp instead of regular FTP The NCBI book will tell you where to download it and how to set it up: https://www.ncbi.nlm.nih.gov/books/NBK158899/ ...
written 7 weeks ago by Philipp Bayer5.8k
0
votes
1
answer
248
views
1
answers
Comment: C: VCF input for KaryotypeR
... >however when I try to convert this to a GRanges object (which I believe is needed for karyotypeR, it does not work. What is the exact error you're seeing? Can you give an example row from your vcf? That example data you have there doesn't look like a vcf ...
written 8 weeks ago by Philipp Bayer5.8k
2
votes
2
answers
156
views
2
answers
Answer: A: Comparing genome assemblies of the same animal
... Mick Watson came up with this simple test for bacterial genomes: http://www.opiniomics.org/a-simple-test-for-uncorrected-insertions-and-deletions-indels-in-bacterial-genomes/ With an N50 of 4,000,000 I don't expect you to have a bacterial genome :) However I don't see why this simple test wouldn't ...
written 11 weeks ago by Philipp Bayer5.8k
0
votes
0
answers
201
views
0
answers
Comment: C: MCScanX empty collinearity file.
... You should have an 'edit' button where you can delete the whole question - but to answer your question, it looks like there's something wrong with the alignments file, the tandem duplications file worked fine but the inter-species comparison is broken, perhaps because the IDs in the gff file are dif ...
written 11 weeks ago by Philipp Bayer5.8k
0
votes
2
answers
312
views
2
answers
Comment: C: Visualizing contig alignment
... I usually remove small contigs (<10kb) because these will only add chaos to the graph anyway. ...
written 3 months ago by Philipp Bayer5.8k
2
votes
2
answers
312
views
2
answers
Answer: A: Visualizing contig alignment
... Are dotplots not an option? Minidot is very fast, but in my experience doesn't work that great with 'bad' assemblies: https://github.com/thackl/minidot Symap is a bit older and slower, but works better with low quality assemblies (again, in my experience), and can also make a circular plot http:// ...
written 3 months ago by Philipp Bayer5.8k
0
votes
3
answers
262
views
3
answers
Answer: A: fastx_collapser: Invalid quality score value (char '/' ord 47 quality value -17)
... Another suggestion: Run Trimmomatic on your data with the TOPHRED33 flag, see whether that'll change your quality scores. ...
written 4 months ago by Philipp Bayer5.8k
1
vote
1
answer
270
views
1
answers
Answer: A: Segmentation fault (core dumped) while running Augustus gene finder on Ubuntu
... Things I would try: - check whether the input file is broken (use `tail` to check the end) - remove small contigs from the assembly (for example, `bioawk -c fastx '{ if(length($seq) > 1000) { print ">"$name; print $seq }}' sandalnew.fa > filtered_sandalnew.fa` ) - recompile augustus via ...
written 4 months ago by Philipp Bayer5.8k
3
votes
1
answer
260
views
1
answers
Answer: A: sorting a BAM file
... That seems to be a very strange read, how can it have a MAPQ > 0? Anyway, you can either try `samtools sort -n` to sort by name, or try setting PICARD's VALIDATION_STRINGENCY to 'lenient', so for example java -jar picard.jar SortSam I=your_input O=your_sorted_output VALIDATION_STRINGENCY=L ...
written 4 months ago by Philipp Bayer5.8k

Latest awards to Philipp Bayer

Popular Question 26 days ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Teacher 10 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
Scholar 3 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Popular Question 3 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
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.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 6 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Popular Question 8 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Popular Question 8 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Good Habit for Bioinformatics Analyst or Scientist
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Appreciated 11 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Teacher 11 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.
Appreciated 12 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Scholar 12 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Popular Question 12 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 938 users visited in the last hour