User: liaoyunshi

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liaoyunshi0
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Posts by liaoyunshi

<prev • 11 results • page 1 of 2 • next >
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(Closed) how to add inline barcode to raw DNA fragment without PCR
... Dear all, I want to use inline barcodes (barcode adjacent to the DNA fragment, included as the starting of the sequencing reads) for my illumina sequencing. Then I found most of current posts used this technique for short amplicon sequencing (e.g. 16S sequencing), in which the inline barcodes can b ...
illumina next-gen sequencing written 5 months ago by liaoyunshi0 • updated 4 months ago by Biostar ♦♦ 20
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How to Get Nucleotide/Allele Frequency Spectrum From NGS SAM/VCF File
... Dear All, I am new to NGS related analysis, so could you help me solve this question? I have **SAM file** from the NGS result of a virus popultion. Then I want get a summary of the **Non-consensus variant frequency spectrum** for the population, just like the panel B of (https://www.ncbi.nlm.nih.g ...
genome frequency next-gen snp written 7 months ago by liaoyunshi0
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Any suggestion for sanger sequencing result editing
... Hi everyone, I just do bi-directional sanger sequencing of my PCR products. I wonder if there is any free software can do the following things 1. check the chromatogram of sequencing results 2. edit the basecalling reads manually 3. automatically align forward and reverse reads, and do the 1. and 2 ...
sanger sequencing chromatogram written 9 months ago by liaoyunshi0 • updated 9 months ago by trausch1.0k
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how to include insertion and deletion in the consensus sequence from BWA reference mapping/assembly
... Many thanks for reading my post. When I finish NGS, I use BWA to conduct reference mapping/assembly to align short reads into the reference genome, and then use samtools and bcftools to get the consensus sequence. Then I found the length of consensus sequence is the same as the reference, with no g ...
genome assembly next-gen alignment sequencing written 10 months ago by liaoyunshi0 • updated 5 months ago by Biostar ♦♦ 20
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How to align new DNA sequences with existing multiple DNA sequence alignment
... Many thanks for reading my post. I want to align some short sequences into an existing multiple sequence alignment of long sequences. The short sequences are partial segments of the long sequences, about 1/10 in length. I think under this situation I should use "**profile alignment**" strategy, an ...
alignment sequence written 10 months ago by liaoyunshi0
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Comment: C: How to align multiple genomic regions simultaneously
... Because I have a huge number of sequences from GenBank. I only know they should be from different regions while I don't exactly know which region each sequence belongs to. So it is hard to separate them at the beginning. Instead, I need to do a huge full alignment at first which can tell me the regi ...
written 10 months ago by liaoyunshi0
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Comment: C: How to align multiple genomic regions simultaneously
... Not very long, about 10-fold in length. But I think the problem is that the MSA program will try to align A/B/C in somewhat overlapping columns, while in fact they should be totally separated because they come from different regions of the genome. ...
written 10 months ago by liaoyunshi0
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Comment: C: How to align multiple genomic regions simultaneously
... Yes, you are right. I want to do a MSA of all sequences at the same time. ...
written 10 months ago by liaoyunshi0
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Comment: C: How to align multiple genomic regions simultaneously
... Thanks for you reply. Actually I want to do a multiple sequence alignment of "reference + A + B + C" at the same time. ...
written 10 months ago by liaoyunshi0
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How to align multiple genomic regions simultaneously
... Many thanks for reading my question. Recently, I want to align multiple sequences from different genomic regions with the whole genome sequences for subsequent phylogenetic study, but I found none of my known tools can fulfill my requirement. Can any fellows give me some suggestion. Thanks a lot. ...
alignment phylogenetics written 10 months ago by liaoyunshi0

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