User: Carambakaracho

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Carambakaracho2.0k
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Bioinformatics specialist at a medical device company

Posts by Carambakaracho

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Comment: C: How to make some modifications to reference genome?
... respectfully, I disagree. chr3:1000100 is col 20 on line 16668 of the chr3 record. I'm not saying it's the best solution, quite on the contrary. It's error prone, tedious to get the coordinates right, text editors struggle with large files, etc... Anyway, my comment was only half serious and most ...
written 24 days ago by Carambakaracho2.0k
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Comment: C: How to make some modifications to reference genome?
... getting more serious, I recommend starting with [Biopython::SeqIO][1]. I never tried to manipulate a genome like you describe (I used Bioperl back then), but at the bottom of the page you might find some useful information in the "Random subsequences" section. I bet you can manipulate the object sim ...
written 25 days ago by Carambakaracho2.0k
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Comment: C: How to make some modifications to reference genome?
... > If programming is necessary, Python solution is preferred. nope. (Almost) any text editor of your choice will do. Use emacs if you want to go completely crazy, vim for a normal level of bioinformatic insanity, Notepad++ for beginners. Trust me, I'm a self-confessed specialist in solving one ...
written 25 days ago by Carambakaracho2.0k
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Comment: C: What form of bacteria genome should we take for filtering
... Do you want to know about bacterial contamination of your otherwise pure human sample or is this about some microbiome? In either case, I fear there's no such thing like a single file. ...
written 4 weeks ago by Carambakaracho2.0k
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Comment: C: what are the big questions in bioinformatics field nowadays
... I understand the field is quite vast for a beginner. I suggest you check on some "big shots" in the field and their research topics, usually you can find their current interests on their websites. Being not academic, my interests are far less basic, so I'm not a big help in identification of those ...
written 4 weeks ago by Carambakaracho2.0k
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Comment: C: NGS reads simulation
... 5 years later, this is still a very impressive list. I have nothing to add but a (unfortunately not so recent) paper that might be of use as additional reference https://dx.doi.org/10.1038%2Fnrg.2016.57 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224698/ Originally posted by [@Joseph Hughes][1 ...
written 4 weeks ago by Carambakaracho2.0k
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Comment: C: NGS data simulation: VarSim or BAMSurgeon?
... Joseph's link is dead, but the paper still valuable: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224698/ or https://dx.doi.org/10.1038%2Fnrg.2016.57 ...
written 4 weeks ago by Carambakaracho2.0k
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Answer: A: how to compare and find similarity between two gene data sets?
... search engines are your friend: https://www.geeksforgeeks.org/python-intersection-two-lists/ ...
written 5 weeks ago by Carambakaracho2.0k
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Comment: C: Tool to check what alternate allele is dominant across samples per line of the V
... :-D damn it, I got the excel shame AND didn't realise the thread was 20 days old. @halo22 you better not use my excel advise and try to hire with Pierre I guess. @pierre or anyone as this is most likely irrelevant for the OP anyway, does biostars feature strikeout markdown? Cheers ...
written 6 weeks ago by Carambakaracho2.0k
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Answer: A: Tool to check what alternate allele is dominant across samples per line of the V
... I made very good experiences with the [bioconductor vcfR package][1]. In case you're new to R, too and this is a one-off project, there's nothing wrong to just use Excel and multiple text-to-column operations to split the data (provided your machine is powerful enough to handle it). It's a bit tedi ...
written 6 weeks ago by Carambakaracho2.0k

Latest awards to Carambakaracho

Scholar 9 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 10 weeks ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Appreciated 5 months ago, created a post with more than 5 votes. For A: BAM/SAM to FASTA conversion
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Scholar 6 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 6 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Scholar 10 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
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Commentator 11 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Scholar 12 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 13 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Calculate CDS phase in gff3 format
Scholar 13 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: How can I calculate the C:N ratio (or just number of carbons and nitrogens) of e
Scholar 15 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
Scholar 16 months ago, created an answer that has been accepted. For A: GTF file for Bombyx Mori
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