User: a.a.kechin

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a.a.kechin20
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Russian Federation
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3 years, 4 months ago
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Posts by a.a.kechin

<prev • 7 results • page 1 of 1 • next >
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Answer: A: can anyone give some example codes to remove primer sequence from MiSeq PCR ampl
... Try cutPrimers that does it: https://github.com/aakechin/cutPrimers. For some question, you can write me or on the github page ...
written 3.4 years ago by a.a.kechin20
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Answer: A: cutadapt software command to trim the primer sequences
... Try cutPrimers: https://github.com/aakechin/cutPrimers. It's specialized on the cutting primer sequences from the NGS reads! If you have any questions on using it, you can contact me ...
written 3.4 years ago by a.a.kechin20
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Comment: C: Contigs unmapped to reference, Sanger sequencing assembly improvements and plasm
... Thank you! I'll try it.  I used a5-miseq pipeline. It produced scaffolds, too. But they were the same as contigs. How to separate contamination from horizontal gene transfer? ...
written 5.7 years ago by a.a.kechin20
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Contigs unmapped to reference, Sanger sequencing assembly improvements and plasmid DNA
... I have paired reads from sequencing bacterial genome with Illumina MiSeq. I assembled them into contigs and now I have 4022 contigs with N50=72749, length of the longest contig 229883, number of mapped contigs 41 and reference genome  (1.8 Mb chromosome + 3 plasmids) coverage 91.35%. And I don't kno ...
assembly next-gen contig sequencing written 5.7 years ago by a.a.kechin20 • updated 5.7 years ago by rob234king600
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Answer: A: What Is A .Ptt File And How It Is Created?
... I've found useful and simple tool for this purpose https://lfz.corefacility.ca/gbk2ptt/ ...
written 5.8 years ago by a.a.kechin20
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Why Do We Need To Set Maximal Read Depth In Samtools
... I analyse reads from Ion Torrent platform with bwa-samtools pipeline. I used them in such way: bwa mem samtools view (convert sam to bam) samtoos sort samtools mpileup bcftools view -bvcg - > var.raw.bcf (call variants as I understand correctly) bcftools view var.raw.bcf | vcfutils.pl varFilter ...
read samtools written 6.9 years ago by a.a.kechin20 • updated 6.9 years ago by Jorge Amigo12k
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Answer: A: Identify Snps For Bacteria - Annotation
... You can use very simple and useful program Procannot: http://www.platform.genexplain.com/procannot/ ...
written 7.1 years ago by a.a.kechin20

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Popular Question 5.5 years ago, created a question with more than 1,000 views. For Why Do We Need To Set Maximal Read Depth In Samtools

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