Find depth of genome

Question

[askari.arezou94]

hello everyone

i have 14 whole genome, but i don't know anything about those coverage and sequencer platform's.

in the first step it is important for me find depth of sequences and in second step ,how can find sequence platform??

thank you

[ATpoint]

Adding on the answer of Mensur Dlakic, where are the data from? Did you generate them (or rather a collaborator), if so ask them. If you have BAM or fastq files the headers of the read names could help narrowing it down, see Illumina Instrument Type from fastq?

For the coverage question please use the search functions, there are many threads on Biostars addressing this, the simplest formula is given in coverage of fastq file and for tools please start with Tools To Calculate Average Coverage For A Bam File? and from there read other threads, this has been asked many times before.

[askari.arezou94]

thank you for good comment.

Answer 1

[Mensur Dlakic]

I could be wrong, but my guess is that there are very few detectives reading posts on this web site. It is impossible to tell the coverage or the sequencing platform from the sequence alone, unless it is provided in FASTA headers. You are in much better position to find this information, as presumably you know the origin of sequences.