User: FatihSarigol

gravatar for FatihSarigol
FatihSarigol100
Reputation:
100
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Trusted
Location:
Durham
Last seen:
1 month, 3 weeks ago
Joined:
1 year, 10 months ago
Email:
s**************@hotmail.com

Posts by FatihSarigol

<prev • 27 results • page 1 of 3 • next >
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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 9 weeks ago by FatihSarigol100
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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 4 months ago by FatihSarigol100
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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 4 months ago by FatihSarigol100
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Comment: C: any tool to join reads regardless of overlap?
... Not sure I understand what you mean, but for merging paired reads for instance there is this tool https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmerge-guide/ ...
written 4 months ago by FatihSarigol100
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Comment: C: BWA MEM -T option. What does really do and how?
... Heng says "-T sets a threshold on the alignment score, not mapping quality. Alignment score is shown in the AS:i: SAM tag. The alignment score is determined by the scoring scheme, which is specified by -A, -B, -O and -E." https://sourceforge.net/p/bio-bwa/mailman/message/30624738/ ...
written 5 months ago by FatihSarigol100
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... This is BRILLIANT! I just tried removing duplicates using few small RADseq and deep full genome fastq files and inspected my results carefully. Simple, transparent, easy & user friendly, memory efficient & pretty fast, and makes a lot of sense doing this to fastq files! I won't criticize the ...
written 5 months ago by FatihSarigol100
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Comment: C: LOSITAN - illegal URL redirect
... aesculus, you can download it together with complete Lositan from the prior page https://github.com/BaskiGIT/lositan you will need some scripting in windows, but I myself cant stop thinking, should we really try to bring a dead program published 10 years ago and apparently abandoned by its owner, ba ...
written 5 months ago by FatihSarigol100
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Answer: A: How does FASTQ format show a diploid sequence.
... It uses the ambiguity codes. For example "nucleotide" Y means that position is heterozygote for C and T nucleotides. If you have a Y in your sliding window, PSMC calls that window to have heterozygosity. SNPs are converted into these IUPAC codes to represent diploid information in a haploid-like si ...
written 6 months ago by FatihSarigol100
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Comment: C: LOSITAN - illegal URL redirect
... I have the same problem, pretty sure never changed my Java version or any of its settings since the last time I ran it successfully few months ago, perhaps nothing we can do and the program is finally down. ...
written 6 months ago by FatihSarigol100
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Comment: C: Problem launching LOSITAN
... I have the same issue, I guess it may have to do with the origin of the software, it works online and needs to connect to its server, that's where it is failing. ...
written 6 months ago by FatihSarigol100

Latest awards to FatihSarigol

Supporter 12 months ago, voted at least 25 times.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Kallisto New RNA-seq quantification method discussion

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