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Search: Posts Made By: Pengfei Liu
Forum: Bioinformatics 10-04-2013, 04:20 AM
Replies: 6
Views: 11,326
Posted By Pengfei Liu
Sorry, I use bwa-mem to do alignment. I have...

Sorry, I use bwa-mem to do alignment. I have tested, in that, -a , -M will affect the output. -a will produce all alignment (so, secondary alignment with 0x100 will appear), and chimeric alignment...
Forum: Bioinformatics 09-15-2013, 10:40 PM
Replies: 6
Views: 11,326
Posted By Pengfei Liu
2 In the bwa-mem document, what does unpaired...

2 In the bwa-mem document, what does unpaired paired-end reads mean(-a parameter description)? what is the differences between it and singleton?

3, does the chimeric alignment get a mapping...
Forum: Bioinformatics 09-15-2013, 10:36 PM
Replies: 6
Views: 11,326
Posted By Pengfei Liu
Thanks so still some additional questions 1,...

Thanks
so still some additional questions
1, I want to use the mapping results of bwa to do Differential expression analysis, what kind of reads should be kept?
1) mapping quality q>threshold(30...
Forum: Bioinformatics 08-28-2013, 01:10 AM
Replies: 6
Views: 11,326
Posted By Pengfei Liu
Post how many mismatches does BWA-MEM tolerate during mapping

Hi,
Recently I am trying to use BWA-MEM to do alignment on PE-90 reads, I have some questiones list as following;


1,how many mismatches does BWA-MEM tolerate during mapping?
Does the...
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