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11.9 years ago
Arpssss
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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 ?
Thanks a lot. Actually issue is suppose hg18 (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/), I download hg18.2bit and from (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/) I download chr1.fa.gz . Now, chromosome should repeated until 22 or should include M,X,Y also ?
It depends. Do you want to map your reads on chrM, chrX and chrY?
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.
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.