User: thackl

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thackl2.6k
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Posts by thackl

<prev • 229 results • page 1 of 23 • next >
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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 6 hours ago by thackl2.6k
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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 6 days ago by thackl2.6k
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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 6 months ago by thackl2.6k
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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 6 months ago by thackl2.6k
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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 6 months ago by thackl2.6k
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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 7 months ago by thackl2.6k
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Comment: C: Merging all sequences with identical ID's
... Ha, just realized, I recommended your tool :) ...
written 7 months ago by thackl2.6k
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Answer: A: Merging all sequences with identical ID's
... `seqkit concat` might do what you want: "concatenate sequences with same ID from multiple files" https://github.com/shenwei356/seqkit ...
written 7 months ago by thackl2.6k
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Comment: C: error for barplot in enrichGO(clusterProfiler)
... Made it bold, an put it in front of the instructions ;) ...
written 9 months ago by thackl2.6k
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Answer: A: error for barplot in enrichGO(clusterProfiler)
... I had the same problem. It is a general problem with the R graphics device. R's default backend for drawing graphics on X11 windows is "Xlib", and that uses the x11-font that doesn't work. From what I understand those x11 fonts are discouraged on current linux distros (not sure about other OS's). ...
written 9 months ago by thackl2.6k

Latest awards to thackl

Scholar 6 days ago, created an answer that has been accepted. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Teacher 3 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 4 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 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
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: PacBio coverage question for a plant genome
Appreciated 16 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: paired end sequencing, sequence distance
Appreciated 22 months ago, created a post with more than 5 votes. For A: PacBio coverage question for a plant genome
Popular Question 2.0 years ago, created a question with more than 1,000 views. For minia assembler - finished with log assembly: 70%
Popular Question 2.4 years ago, created a question with more than 1,000 views. For minia assembler - counting kmers 'gatb::core::system::Exception'
Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Good Answer 3.0 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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