User: thackl

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thackl2.7k
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Posts by thackl

<prev • 233 results • page 1 of 24 • next >
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Comment: C: Get BUSCO gene descriptions
... Yeah, I was hoping you had moved on by now ;) ...
written 6 weeks ago by thackl2.7k
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Answer: A: Get BUSCO gene descriptions
... Just came across the same issue, and came up with a solution. Most BUSCO data sets are generated from OrthoDB. You can query OrthoDB via its API to map BUSCO IDs and pull the information. I've posted a short R snippet to automate this and produce a nice table https://thackl.github.io/BUSCO-gene-desc ...
written 6 weeks ago by thackl2.7k
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Comment: C: retrieve multiple bacterial genes and flanking regions
... OK, this worked for me on a dummy example. Minor fixes to old code & strip the flank annotations from IDs. Only problem, the final file doesn't contain "gene names" but id as chr:start-end... seqkit subseq --up-stream 200 --down-stream 200 --gtf genome.gff genome.fna > all-orfs-with-flanks.ff ...
written 12 weeks ago by thackl2.7k
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Comment: C: retrieve multiple bacterial genes and flanking regions
... Hmm, you're right. seqkit uses coordinates for ids instead of the gene_id from the gff... Hadn't thought about that. I don't have an easy fix for that atm. Need to think about it ...
written 12 weeks ago by thackl2.7k
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Comment: C: retrieve multiple bacterial genes and flanking regions
... Yes, something like the snippet below could work. Needs one little extra piece of command line magic, though. I'm assuming you are working on a bash-like command line: # get orfs with flanks as before seqkit subseq --up-stream 200 --downstream 200 --gtf genome.gff genome.fa > all-orfs-with-flank ...
written 3 months ago by thackl2.7k
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Answer: A: retrieve multiple bacterial genes and flanking regions
... Have a look at https://github.com/shenwei356/seqkit and its subseq command: "get subsequences by region/gtf/bed, including flanking sequences". All you need is fasta file of you genome of interest and a gff file (gene annotations). Command could look like this: seqkit subseq --up-stream 200 --d ...
written 3 months ago by thackl2.7k
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Answer: A: Calculate CG content in a fastq file
... `sed -n '2~4p' file.fastq | tr -d aAtTnN"\n" | wc -c` should do if you want to stick as close as possible to your fasta example. Probably not the best way though. ...
written 10 months ago by thackl2.7k
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Comment: C: Printable visualizations of large-scale alignments
... When you say convert to PDF, do you want them to still be vector graphics? Or would bitmaps work too? ...
written 10 months ago by thackl2.7k
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Comment: C: Printable visualizations of large-scale alignments
... Ah, good to know. Haven't used it for alignments that big yet. ...
written 10 months ago by thackl2.7k
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Answer: A: Printable visualizations of large-scale alignments
... If you want PDF, there's are powerful latex package: http://ftp.cvut.cz/tex-archive/macros/latex/contrib/texshade/texshade.pdf And if you don't want to deal with tex, there's an R interface, too: https://rdrr.io/bioc/msa/man/msaPrettyPrint.html ...
written 10 months ago by thackl2.7k

Latest awards to thackl

Voter 6 weeks ago, voted more than 100 times.
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Scholar 3 months ago, created an answer that has been accepted. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Appreciated 19 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Popular Question 2.3 years ago, created a question with more than 1,000 views. For minia assembler - finished with log assembly: 70%
Popular Question 2.7 years ago, created a question with more than 1,000 views. For minia assembler - counting kmers 'gatb::core::system::Exception'
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Good Answer 3.3 years ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
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Scholar 3.7 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance
Appreciated 3.8 years ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Commentator 3.9 years ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Scholar 3.9 years ago, created an answer that has been accepted. For A: paired end sequencing, sequence distance

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