User: bbb

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bbb60
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60
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New User
Location:
Russian Federation
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2 years, 5 months ago
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3 years, 11 months ago
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Posts by bbb

<prev • 7 results • page 1 of 1 • next >
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which alignment tool is better to use to align genome on short reference sequence ~5000b.p
... I have `22` reference sequences with length about `5000 b.p.` Which alignment tool is better to use to align genome on short reference sequence? Is `bwa-MEM` the preferred algorithm? I used `bowtie2`, however it doesn't supposed to work good enough with short reference sequence. ***From bowtie2 ...
bowtie2 alignment bwa use written 2.5 years ago by bbb60
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Clustering by sequence alignments
... Which cluster method is better to use to cluster DNAs of different species based on alignment information (matches, deletions, insertion)? i.e. reference sequence - sequence of 4000 b.p. length, then feature set is 4000 * |{b.p. from reads which was matched exactly, b.p. insertions, deletions}| = 12 ...
alignment clustering dna written 2.5 years ago by bbb60 • updated 7 months ago by Biostar ♦♦ 20
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How to determine if a sequence is nonsatellite sequence?
... How to determine if a sequence is nonsatellite sequence? For example, I want to determine insertion of nonsatellite sequences in reads ...
satellite sequence dna written 2.5 years ago by bbb60 • updated 2.5 years ago by Biostar ♦♦ 20
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Full-length HOR sequences
... Where can I find full length HOR sequences (in fasta etc)? For example, in [this][1] article there is reference to full length HOR seqence of DXZ1 and DYZ3 arrays: >Complete HuRef WGS read libraries for both DXZ1 and DYZ3 arrays were obtained from alignment to full-length HOR sequences that were ...
alpha-satellite fasta hor written 2.5 years ago by bbb60
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How to get the consensus sequence from a BAM alignment
... How to convert bam to fasta? I have bam files and reference fasta. I want to get fasta sequence from bam file: ![see picture][1] Is there a software that can do this? [1]: http://s22.postimg.org/hwdzkaktt/fasta.png ...
fasta bam dna written 3.5 years ago by bbb60 • updated 3.5 years ago by Istvan Albert ♦♦ 81k
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1000 genomes project mitochondrial DNA sequences
... Help! How (where) to get mitochondrial dna sequences from "1000 genomes" project? This is what I found: http://www.1000genomes.org/announcements/phase3-mitochondrial-chromosome-variants-now-available-2015-10-06/ http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/README_chrMT_phase3_call ...
mtdna sequence 1000genomes written 3.5 years ago by bbb60 • updated 3.5 years ago by Shane McCarthy320
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Bowtie2 reporting alignments count
... I am using bowtie2 for mapping genome to reference fasta. As said in bowtie2 manual it reports only the best one alignment. What if read has two best alignments with the same score?  Will it report only one random read? ...
genome alignment written 3.9 years ago by bbb60 • updated 3.9 years ago by Thibault D.650

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Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to get the consensus sequence from a BAM alignment

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