User: FatihSarigol

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FatihSarigol140
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Posts by FatihSarigol

<prev • 36 results • page 1 of 4 • next >
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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 6 months ago by FatihSarigol140
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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 6 months ago by FatihSarigol140
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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 8 months ago by FatihSarigol140
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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 9 months ago by FatihSarigol140
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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 9 months ago by FatihSarigol140
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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 9 months ago by FatihSarigol140
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Comment: C: How to extract specific chromosome from vcf file
... This worked well for me, too! For many chromosomes, do: -R, --regions-file restrict to regions listed in a file ...
written 9 months ago by FatihSarigol140
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Comment: C: Convert from PSL to MAF
... Cool! For anyone with an issue with BioPython, here is an alternative from CGAT: https://github.com/CGATOxford/cgat/blob/master/CGAT/scripts/psl2gff.py ...
written 9 months ago by FatihSarigol140
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Answer: A: Mismatch and Indel statistics from BAM/SAM file
... Try [Qualimap2][1] [Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data][2] [1]: http://qualimap.bioinfo.cipf.es [2]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4708105/ ...
written 12 months ago by FatihSarigol140
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Comment: C: Substituting Snps On Reference Genome Assemblies
... Hi Natalia, I guess this is a question for my code up there. That 8000 was the default value of maximum depth selected by samtools mpileup (I just checked it still seems to be the same in the manual) I guess I had written that to indicate an available option that is sometimes important to change, no ...
written 17 months ago by FatihSarigol140

Latest awards to FatihSarigol

Popular Question 5 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 9 months ago, voted more than 100 times.
Supporter 2.3 years ago, voted at least 25 times.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Kallisto New RNA-seq quantification method discussion

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