Moderator: Philipp Bayer

gravatar for Philipp Bayer
Philipp Bayer4.2k
Reputation:
4,250
Status:
Trusted
Location:
Australia/Perth/UWA
Twitter:
PhilippBayer
Last seen:
49 minutes ago
Joined:
5 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 • 344 results • page 1 of 35 • next >
0
votes
1
answer
163
views
1
answers
Comment: C: trying to use gnu parallel and blast
... Good to see it works for you :) ...
written 2 days ago by Philipp Bayer4.2k
1
vote
1
answer
163
views
1
answers
Comment: C: trying to use gnu parallel and blast
... I just tried it with some made-up test data and it works fine for me, I get the output that I expected - what is the error you're seeing? ...
written 3 days ago by Philipp Bayer4.2k
0
votes
1
answer
148
views
1
answers
Answer: A: How to convert .gff3 to .gff
... Normally a gff3 file and a gff file should be indistinguishable to most parsers (in fact often a gff file is a gff3 file, but not always), do you get an error in Gff2GeneTable when you load your gff file? Have a look at what a gff3 validator tool such as [this one][1] tells you about your gff file, ...
written 3 days ago by Philipp Bayer4.2k
0
votes
1
answer
105
views
1
answers
Answer: A: error in cuffmerge
... I haven't encountered this before, but it looks like it doesn't like the () in the file name for '/home/mra/Desktop/ensan/Homo-sapiens(hg19).fa'? Have you tried just renaming that file, removing those brackets? ...
written 4 days ago by Philipp Bayer4.2k
2
votes
1
answer
81
views
1
answers
Answer: A: RepeatMasker in Maker
... I assume that option is the '-nolow' flag in RepeatMasker ([ref][1]). By default it's not too easy to get non-standard flags into RepeatMasker, in the past I think there was a way to get no_low into RepeatMasker directly, looking at the code in the maker folder in `lib/GI.pm`: runRepeatMask ...
written 6 days ago by Philipp Bayer4.2k
0
votes
1
answer
124
views
1
answers
Comment: C: Help needed interpreting/integrating WebMGA KOG results onto transcriptome (FAST
... I see! I slightly changed the code - I now use a defaultdict, which by default stores an empty list for any possible key, so I can just append to that. I run it like this: python3 compare.py KOG.2 FASTA.fasta Code is: from Bio import SeqIO import sys from collections import defa ...
written 7 days ago by Philipp Bayer4.2k
1
vote
0
answers
86
views
0
answers
Comment: C: Excel Files corrupted in R.
... That's about it! An xlsx file is a compressed archive of your data, while read.table() assumes that your input data is uncompressed, flat text. The garbled text you're seeing is compressed binary. The xlsx package can read that. ...
written 7 days ago by Philipp Bayer4.2k
0
votes
1
answer
124
views
1
answers
Answer: A: Help needed interpreting/integrating WebMGA KOG results onto transcriptome (FAST
... Hmm I'd do this using Biopython because it's easier. The following assumes that the kog file fits into memory, is tab-delimited, and has the gene name in column 1. It's also got bad argumentparsing, argparse would be the way to go. It's untested. from Bio import SeqIO import sys ...
written 10 days ago by Philipp Bayer4.2k
1
vote
1
answer
70
views
1
answers
Answer: A: what edits to make on maker_opts to predict complete genes using MAKER
... This is the code that is triggered: #walk out edges to force completion if($CTL_OPT->{always_complete} && (!$has_start || !$has_stop)){ $f = PhatHit_utils::adjust_start_stop($f, $seq); $transcript_seq = get_transcript_seq($f, $seq); ($translation_seq, $ ...
written 15 days ago by Philipp Bayer4.2k
1
vote
1
answer
118
views
1
answers
Answer: A: Converting a big SNP genotype table to plink (.ped) file for ADMIXTURE
... Your table looks non-standard to me so I don't think there's a publicly available parser, but I might be wrong. Here are some rules to get you going with your own parser, you'll have to transpose that table and add a few columns like you have them there. - Only the combination of family and indivi ...
written 23 days ago by Philipp Bayer4.2k

Latest awards to Philipp Bayer

Appreciated 24 days ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Scholar 24 days ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 24 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 4 weeks ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Scholar 10 weeks ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 12 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
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Epic Question 4 months ago, created a question with more than 10,000 views. For Best Way To Get Truly Unique Reads In Bowtie/Sam?
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 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.
Appreciated 10 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Scholar 10 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Good Answer 10 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!
Scholar 11 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 11 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
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: 853 users visited in the last hour