User: FatihSarigol

gravatar for FatihSarigol
FatihSarigol170
Reputation:
170
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Trusted
Location:
Durham
Website:
https://www.researchga...
Last seen:
1 week, 3 days ago
Joined:
3 years, 9 months ago
Email:
s**************@hotmail.com

Posts by FatihSarigol

<prev • 40 results • page 1 of 4 • next >
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Comment: C: How do you cite a tool that doesn't have a publication?
... Forgetting or ignoring to cite is one thing but there is also the problem with number of reference limits some journals have for some brief formats which sadly makes it impossible to cite every single tool used in the study properly. Perhaps tools should be excluded from such limits. ...
written 14 days ago by FatihSarigol170
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Answer: A: Tool to generate proportional Venn Diagrams?
... This one is sort of new and gives perfectly proportional venn diagrams: [Using nVennR to generate and explore n-dimensional, quasi-proportional Venn diagrams][1] It can also calculate the common/unique members of different groups from a single list.. [1]: https://cran.r-project.org/web/package ...
written 9 weeks ago by FatihSarigol170
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Comment: C: How to identify the bp distance of blast results to closest genes in a genome
... thanks! though if you meant it works directly, probably something is odd about my blastplus version, it did require some parsing for my output format 6, but I got it to work anyway. great tool to have! ...
written 10 weeks ago by FatihSarigol170
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How to identify the bp distance of blast results to closest genes in a genome
... Using the blastplus output blasted against a single species genome database prepared locally, for each blast hit, I want to search the GFF annotation file to ask how far away the hit is to the closest gene in this genome. Easy to check manually for a few hits, but I need a program that can do it a ...
genome sequence blast written 11 weeks ago by FatihSarigol170
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Comment: C: vcftools Warning: Expected at least 2 parts in FORMAT entry
... thank you :D so, nothing to worry I see ...
written 15 months ago by FatihSarigol170
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Comment: C: vcftools Warning: Expected at least 2 parts in FORMAT entry
... I just had the same thing as well strangely ...
written 16 months ago by FatihSarigol170
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Answer: A: Split fai (fasta index) or VCF into N nearly equal total length chunks
... I wrote a code that does exactly what I want, if anyone else needs a similar thing, you can find it [here][1] [1]: https://github.com/FatihSarigol/LittlePrograms/blob/master/FASTAindexSPLITTERinEQUALsize.sh Run it as ./FASTAindexSPLITTERinEQUALsize.sh samtoolsExecutable fastaFile numberOf ...
written 18 months ago by FatihSarigol170
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Comment: C: Split fai (fasta index) or VCF into N nearly equal total length chunks
... thanks, very similar actually, but I can't split the chromosome into chunks, I need 1 scaffold to exist only in 1 file, and I am only interested in total size of the scaffold. I am trying to do it on an fai file using awk now; will post my code here if I manage. ...
written 18 months ago by FatihSarigol170
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Comment: C: Split fai (fasta index) or VCF into N nearly equal total length chunks
... Thanks for your comment. Yes the fai itself is small, but the jobs I want to run on the total VCF take so long time, and I need this to be able to split the VCF into nearly equal chunks. I used to do this by manually splitting the fasta index by eyeballing, but I need to make a program or code do th ...
written 18 months ago by FatihSarigol170
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Split fai (fasta index) or VCF into N nearly equal total length chunks
... It is easy to do it manually on your favorite genome, but I need to write a code that can split a fasta index into sets of scaffolds in the same order, based on size. An example would be (only using the first 2 columns of an fai file): Scaffold1 100 Scaffold2 50 Scaffold3 200 Scaffold4 500 ...
genome faidx written 18 months ago by FatihSarigol170

Latest awards to FatihSarigol

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Kallisto New RNA-seq quantification method discussion
Popular Question 15 months ago, created a question with more than 1,000 views. For Aligning Reads with Overhangs on the Ends (Edges) of Reference Contigs or Scaffolds
Voter 18 months ago, voted more than 100 times.
Supporter 3.0 years ago, voted at least 25 times.
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Kallisto New RNA-seq quantification method discussion

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