User: FatihSarigol

gravatar for FatihSarigol
FatihSarigol160
Reputation:
160
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Location:
Durham
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https://www.researchga...
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5 hours ago
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3 years, 7 months ago
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Posts by FatihSarigol

<prev • 38 results • page 2 of 4 • next >
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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 18 months ago by FatihSarigol160
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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 23 months ago by FatihSarigol160
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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 2.2 years ago by FatihSarigol160
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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 2.2 years ago by FatihSarigol160
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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 2.2 years ago by FatihSarigol160
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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 2.2 years ago by FatihSarigol160
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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 2.2 years ago by FatihSarigol160
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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 2.3 years ago by FatihSarigol160
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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 2.3 years ago by FatihSarigol160
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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 2.3 years ago by FatihSarigol160

Latest awards to FatihSarigol

Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Kallisto New RNA-seq quantification method discussion
Popular Question 12 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 16 months ago, voted more than 100 times.
Supporter 2.8 years ago, voted at least 25 times.
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Kallisto New RNA-seq quantification method discussion

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