User: kamanovae

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kamanovae0
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Posts by kamanovae

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Comment: C: How to use BBmap (mutate.sh) to simulate the human genome?
... At this stage, I need to introduce mutations in the reference genome, and then I plan to use the NanoSim program to simulate nanopore reads. My final goal is nanopore reads with introduced mutations. Which program is better for the first step? ...
written 11 weeks ago by kamanovae0
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How to use BBmap (mutate.sh) to simulate the human genome?
... Hi! I want to simulate the human genome. I found a suitable BBMap (mutate.sh) program. The mutate.sh only outputs reads that contain mutations. But I need to get a fast output file that would contain reads with mutation and without mutations. I want to try to maintain the coverage of the reference g ...
human genome simulation bbmap written 11 weeks ago by kamanovae0 • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: Why Samtools view don't extract sequence out of the given region?
... I appreciate your help! Can I use the Samtools view to get only the necessary region, if now I need to extrect the sequence? ...
written 11 weeks ago by kamanovae0
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Why Samtools view don't extract sequence out of the given region?
... Hi! I have nanopore sequencing results in fastq format. I need to know the coverage of specific genes. To do this, I aligned the sequence using minimap2 and converted the result to bam format. I want to use the Samtools view to extract the gene by coordinate. Then I plan to use the Samtools depth. ...
samtools view written 11 weeks ago by kamanovae0 • updated 11 weeks ago by finswimmer13k
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Comment: C: How to convert a file to vcf format
... Thanks for the answer! I painted my question poorly. I need to create a file for each sample. It is necessary to get information about specific SNPs for a sample from each file of a certain chromosome and write it in a separate VCF file. I hope that there are ready-made programs for this ...
written 11 months ago by kamanovae0
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How to convert a file to vcf format
... Hello, I have a file for each chromosome that represents the following format: CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 Sample3 10 62010 10:62010 C T 999 PASS SING;AA=NN;AN=CC;AD=CC GT 0|0 0|0 0|0 ...
vcf combine file written 11 months ago by kamanovae0 • updated 11 months ago by Pierre Lindenbaum129k
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Why do researchers prefer to use Oxford Nanopore Technologies' 1D and sequencing rather than 1D2 when sequencing the human genome?
... Hello everyone, I want to sequence the human genome using Oxford Nanopore Technology. I came across various papers of ONT in the year 2019 on this topic and in all studies use 1D protocols technology, not 1D2. I listed the most popular articles here: 1) https://www.nature.com/articles/nbt.4060#met ...
human genome sequencing nanopore ont written 11 months ago by kamanovae0
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How can I ran Samtools view in Cancer Genomics Cloud (Simons Genome Diversity Project)?
... Hi! I have created a project on Cancer Genomics Cloud (Simons Genome Diversity Project). Next I have downloaded SAMtools view in Apps in this project. The input file for task were : 1) The Bam file from Simons Genome Diversity Project (for example: LP6005442-DNA_B02.srt.aln.bam). As I understand th ...
cgc samtools view written 21 months ago by kamanovae0

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