User: stolarek.ir

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stolarek.ir530
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Posts by stolarek.ir

<prev • 115 results • page 1 of 12 • next >
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Comment: C: Illumina paired end read header difference- SPAdes bwa run ERROR
... download bbmap and use repair.sh from it like so: ./repair.sh in1=pair1.fastq in2=pair2.fastq out1=out_pair1.fastq out2=out_pair2.fastq outsingle=out_single.fastq ...
written 5 days ago by stolarek.ir530
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Comment: C: RNASeq lane effect
... there might be something off if you multiplex hardly, and the indexes used within the lane do not co-op with each other well ...
written 5 days ago by stolarek.ir530
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Comment: C: long reads Pacbio SNP calling
... either look at their webpage if they have anything dedicated for that, or use GATK ...
written 13 days ago by stolarek.ir530
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Answer: A: long reads Pacbio SNP calling
... no worries, with high coverage you can do a decent SNP calling using PacBio ...
written 13 days ago by stolarek.ir530
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codeml, output tree topology different from the input tree
... Dear all, I am struggling with understanding the output of the codeml. I used typical M0 model with settings like so: runmode = 0 seqtype = 1 CodonFreq = 2 clock = 0 model = 0 NSsites = 0 The provided tree (runmode = 0) is however severely altered in the o ...
paml codeml written 15 days ago by stolarek.ir530
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Comment: C: Paired vs unpaired (DNA Sequencing)
... cmon, at least use google and read about anything on the first page ...
written 6 weeks ago by stolarek.ir530
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Comment: C: How to align multiple genomic regions simultaneously
... I don't really get it. Is the problem that aligner takes one read and maps it? This is how it's done, alignment of each read is independent from other reads ...
written 7 weeks ago by stolarek.ir530
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Answer: A: PLINK RECODING ISSUE
... the way I do it is to first genotype the vcf files I have with a common set of SNPs (in other words genotype against a list of SNP positions, so that every individual genotyped is going to have the same number of markers). bedtools intersect -a my.vcf -b bed_present_snps -wa -header > out.v ...
written 7 weeks ago by stolarek.ir530
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Comment: C: Ancestry Informative Markers
... not really. If you have everything set up correctly (the genome versions are the same - thus, the positions of markers correspond between reference samples and your samples) you can even use plink to select only the markers that you want (by these I mean the markers from reference file). This is als ...
written 7 weeks ago by stolarek.ir530
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Comment: C: Ancestry Informative Markers
... You can always go and search google for AIMs, but that will give you a set of 20 or 200 markers, which are good for broad continental distinctions. A better approach could be to genotype against some big set of good markers, for example Human Origins set (about 600k markers) or markers derived from ...
written 7 weeks ago by stolarek.ir530

Latest awards to stolarek.ir

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Genotype Likelihoods
Popular Question 3 months ago, created a question with more than 1,000 views. For plink 1.9 PED to VCF, SNPs differ on input and output files
Popular Question 5 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Centurion 5 months ago, created 100 posts.
Popular Question 5 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Genotype Likelihoods
Popular Question 12 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Split Reads vs Supplementary Reads
Popular Question 20 months ago, created a question with more than 1,000 views. For Python Cigar String - Finding Indels Break Points Positions
Popular Question 21 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Popular Question 22 months ago, created a question with more than 1,000 views. For Extract Regions Of Genome That Have 0 Coverage
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Python Cigar String - Finding Indels Break Points Positions
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Python - Scan Thorugh A Large File And Report Matches In Vcf File Under Conditions

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