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Old 03-27-2016, 08:28 PM   #1
yong peng
Junior Member
 
Location: China

Join Date: Mar 2016
Posts: 1
Question remove scaffold and other unplaced sequence before mapping?

Hi,
I downloaded reference genomes from Ensembl (fasta format). But there are lots of sequences with name "dna:scaffold": https://github.com/CTLife/TEMP/tree/master/RefGenomes

Such as Mouse_GRCm38 (mm10), except chromosome 1-19, Mt, X and Y; others should be removed before mapping ? https://github.com/CTLife/TEMP/blob/..._GRCm38.p4.txt

Such as Human_GRCh38.p5 (hg38), https://github.com/CTLife/TEMP/blob/..._GRCh38.p5.txt, there are 516 sequences. In addition to chromosome 1-22, Mt, X and Y; others (such as CHR_HG2241_PATCH and KI270728.1) should be removed before mapping ?

Last edited by yong peng; 03-27-2016 at 08:30 PM.
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analysis, bioinfomatics, mapping, next gen sequencing, reference genome

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