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Full Genomic Database And Corresponding Chromosomal Databases

I am doing some experiment using BowTie and Q-Pick which are short read aligners that aligns short DNA sequences (reads) to the human genome. However, one works with full Human genomic database and another works with it's corresponding chromosomal databases (for chromosome 1,2, 3....). Now from here, I found full Human Genome Database for h19. However, can't understand where is it's corresponding chromosomal databases are. Can anybody help me how to solve this issue ?

bowtie bowtie2 genome
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updated by Vikas Bansal Vikas Bansal • written by Arpssss • Arpssss

1 answer

If you want hg19 dataset according to chromosomes (fasta file for each chromosome), you can click on "Data set by chromosome" from link you mentioned. link for hg19 . Link for hg18.

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written by Vikas Bansal Vikas Bansal

It depends. Do you want to map your reads on chrM, chrX and chrY?

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written by Vikas Bansal Vikas Bansal

No, I don't. Suppose I download 1-22 chromosomes and concatenate those files in a single file and give input to the tool. Is it acceptable ? Means does Concatenated all chromosome files == Full Genomic database ? I have no idea in BioInfo, sorry if I am asking stupid questions.

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written by Arpssss • Arpssss

Firstly I would say no questions are stupid but one should always try to find out answer before asking because it will also make you learn lot of other things. So if you want to map your reads to 1-22 chr, then yes you can concatenate.

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written by Vikas Bansal Vikas Bansal

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