User: ALchEmiXt

gravatar for ALchEmiXt
ALchEmiXt1.7k
Reputation:
1,700
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Location:
(close to) Lelystad, The Netherlands
Website:
http://www.wur.nl/biov...
Twitter:
a_bossers
Scholar ID:
Google Scholar Page
Last seen:
2 days, 9 hours ago
Joined:
5 years, 8 months ago
Email:
a***********@wur.nl

Working mainly on multi-Omics approaches using all kinds of OMICS tools, metagenomics, meta-transcriptomics, NGS and bioinformatics.
Linux enthousiast. Preferred languages/platforms: Perl, R, PHP, BASH, Ubuntu, galaxy
Occasionally you can find me on Twitter as well.
CU,
Alex

Posts by ALchEmiXt

<prev • 204 results • page 1 of 21 • next >
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Comment: C: Converting Uniprot File to a Fasta File in Perl
... PS: I assume you just provided an example FASTA right? Since that FASTA is nucleotide space and not protein like the Swissprot. If you need nucleotide you need to follow accessions to a different DB type. ...
written 2 days ago by ALchEmiXt1.7k
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Comment: C: Converting Uniprot File to a Fasta File in Perl
... no actually your regexp grab tries to catch everything at once. This is not possible for the multiple line data after the SEQ element. There you need to continue grabbing lines until either a end delimiter like // or till EOF. ...
written 2 days ago by ALchEmiXt1.7k
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Comment: C: dedupe from BBMAP suite woes with memory and stdout
... Just learned about the clumpify tool. Thanks and keep up the good work. Appreciated! Shouldn't stderr return empty unless there is an error? So why not printing to stdout? ...
written 3 days ago by ALchEmiXt1.7k
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Comment: C: dedupe from BBMAP suite woes with memory and stdout
... clumpify might indeed do what I want. I did play around with the clusterstats file but didn't get what I expected. I will reinvestigate it. ...
written 3 days ago by ALchEmiXt1.7k
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Answer: A: Converting Uniprot File to a Fasta File in Perl
... Without writing the full answer from this tablet... bioperl might be the best way to go. like commented. However if you do want to do it line by line and performance doesn't seem to be an issue.... approach it as follows: 1) read the file line by line like you do. 2) first check for each id like ...
written 3 days ago by ALchEmiXt1.7k
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dedupe from BBMAP suite woes with memory and stdout
... Working with dedupe from the BBMAP suite (highly appreciated suite!) to estimate/determine exact duplicates in Illumina PE150 metagenomic data. Potential overamplification bias in PCR at library prep. Two things I hope to get some clues on: 1) can dedupe output the console output to a stats file? ...
duplicates fastq bbmap dedupe linux written 3 days ago by ALchEmiXt1.7k • updated 3 days ago by Brian Bushnell9.8k
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Comment: C: NCBI: batch upload WGS sequences linked to bioproject/biosample
... Actually I don't have a batch solution yet. At that time we solved it by going through all steps by hand in batches. At least the involved PhD did... Have to refresh this since we will be facing another batch of 1000+ genomes this year. Heard the EBI tools might be more flexible but didn't check it ...
written 3 days ago by ALchEmiXt1.7k
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Comment: C: samtools mpileup not calling small (6 base) INSERT
... will check that and post back later. ...
written 5 months ago by ALchEmiXt1.7k
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Comment: C: samtools mpileup not calling small (6 base) INSERT
... no not yet. I had to give it a rest for a while, but it still puzzles me. ...
written 5 months ago by ALchEmiXt1.7k
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Comment: C: How can I run All-v-all BLAST
... oh my bad. Seems orthoMCL is an ortholog classifier... ...
written 8 months ago by ALchEmiXt1.7k

Latest awards to ALchEmiXt

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Best Way To Close Gaps In Genome With Single Reads
Popular Question 6 months ago, created a question with more than 1,000 views. For Contaminant Filtering Large Fastq Data Sets
Popular Question 8 months ago, created a question with more than 1,000 views. For Contaminant Filtering Large Fastq Data Sets
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Great Question 12 months ago, created a question with more than 5,000 views. For Contaminant Filtering Large Fastq Data Sets
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: How To Draw Genome Features Along Chromosome
Scholar 16 months ago, created an answer that has been accepted. For A: Average coverage of de novo SPAdes assembly deviates a lot from theretical cover
Good Question 22 months ago, asked a question that was upvoted at least 5 times. For Contaminant Filtering Large Fastq Data Sets
Popular Question 22 months ago, created a question with more than 1,000 views. For Contaminant Filtering Large Fastq Data Sets
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Contaminant Filtering Large Fastq Data Sets
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How Common Are Multi-Line Fastq Files?
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Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Best Way To Close Gaps In Genome With Single Reads
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Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Best Way To Close Gaps In Genome With Single Reads
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Mapping Reads Back To Assembly Contigs
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: How To Draw Genome Features Along Chromosome
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