remove scaffold and other unplaced sequences before mapping ?

[CTLife]

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/master/RefGenomes/Mouse_GRCm38.p4.txt

Such as Human_GRCh38.p5 (hg38), https://github.com/CTLife/TEMP/blob/master/RefGenomes/Human_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 ?

[billzt]

I even encounter some draft assemblies with thousands of scaffolds besides the main chromosomes

[CTLife]

@billzt These thousands of scaffolds besides the main chromosomes need to be removed before mapping ChIP-seq and RNA-seq reads ? ?

[billzt]

Well, usually I'll kept them.

[CTLife]

Thank you.