Transfer a whole genome with .bam format

[wuhoucdc]

Dear all,

Do you have experience to transfer a whole genome of short-reads with ~35X sequenced by Illumina GA to .bam format using samtools? I feel very strange when I got more than 500G data. I addition, how can you extract chromosomes one by one and sort as well as index them? Thank you very much!

Wuhoucdc

[dawe]

Dear all,

Do you have experience to transfer a whole genome of short-reads with ~35X sequenced by Illumina GA to .bam format using samtools? I feel very strange when I got more than 500G data. I addition, how can you extract chromosomes one by one and sort as well as index them? Thank you very much!

Wuhoucdc

Never had a whole genome with that coverage :-( Sorted BAM may be slightly smaller.
To extract a single chrom (or a single region) index it

samtools index file.bam

and then extract your region

samtools view file.bam chrom[:start-end]

HTH

d

[wuhoucdc]

Thanks for your answer, dawe.

But why did you say "Never had a whole genome with that coverage "? Most of the sequenced individuals such as YH (PMID:18987735) and AK1 (PMID:19587683) were higher than that coverage (>35X).

Wuhoucdc

[dawe]

Thanks for your answer, dawe.

But why did you say "Never had a whole genome with that coverage "? Most of the sequenced individuals such as YH (PMID:18987735) and AK1 (PMID:19587683) were higher than that coverage (>35X).

Wuhoucdc

:-) I usually deal with ChIP-seq or exome analysis, never had a "first hand" high coverage of human genome.
d