User: Baoxu

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Baoxu0
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Posts by Baoxu

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Fusion detection tool error (STAR-fusion, STAR-SEQR,arriba)
... For the Star-fusion, have you downloaded the dfamscan.pl? Make sure the path of dfamscan.pl is in the ENV PATH and have the Executable mode(chmod +X) ...
written 4 months ago by Baoxu0
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Answer: A: Zero Trace error running Eigenstrat 5
... I encounter same problem: here's mistakes I made: the smartpca need 3 files (ind snp genols) files , check the snp files and make sure the style of chr name is right. (e.g. chr1 chr2 ) because I use Mt chr1A names and smartpca can not recognize them ...
written 9 months ago by Baoxu0
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How to define haplogroup in plant
... The haplogroup in human is often determined by snps in mitochondria. Recently I have to divide the population of a kind of plant into different types of haplogroup using the mitochondria snps. I found two references using different kinds of method in plants: one is in Arabidopsis- they use QT-clust ...
genome snp sequencing written 10 months ago by Baoxu0 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: Polyploid genome and mapping !!
... Many thanks for your reply! I don't understand what you mean for the first option. Maybe I didn't explain the question well. I mapped the re-sequencing reads(100 bp pair-end) with bwa-mem (defaut parameter) for the hexaploid wheat. But I found a lot of reads which can be mapped to reference have ...
written 11 months ago by Baoxu0
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Answer: A: Polyploid genome and mapping !!
... Same questions! When the reference is tetraploid or hexaploid there are many duplications across the genome. Lots of reads will be Mutipul-mapped reasds. How to deal with it ? ...
written 11 months ago by Baoxu0
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Answer: A: What Causes The Bwa Error: "Assertion `Re - Rb == Rlen' Failed."
... It seems that some of reads in fastq have some problem. I suspect the some of the reads may be too short ( < 30bp). ...
written 11 months ago by Baoxu0

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