User: FatihSarigol

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FatihSarigol120
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Posts by FatihSarigol

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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 3 days ago by FatihSarigol120
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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 11 days ago by FatihSarigol120
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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 11 days ago by FatihSarigol120
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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 11 days ago by FatihSarigol120
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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 13 days ago by FatihSarigol120
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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 4 weeks ago by FatihSarigol120
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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 3 months ago by FatihSarigol120
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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 8 months ago by FatihSarigol120
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Comment: C: Samtools faidx non-zero exit status 217
... Just wondering, does samtools itself work when you type samtools? As the manual says, "if a command is not found, the child process created to execute it returns a status of 127" [GNU][1] [1]: https://www.gnu.org/software/bash/manual/html_node/Exit-Status.html ...
written 10 months ago by FatihSarigol120
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Comment: C: Extracting allel, Genotype from VCF file
... how about [VCFtools][1]? [1]: https://vcftools.github.io/man_latest.html ...
written 10 months ago by FatihSarigol120

Latest awards to FatihSarigol

Voter 21 days ago, voted more than 100 times.
Supporter 18 months ago, voted at least 25 times.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Kallisto New RNA-seq quantification method discussion

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