Question: Giga base or Giga byte
gravatar for Shawrob400
12 weeks ago by
Shawrob4000 wrote:

Hi I am a student from genomic research group,CVASU,Chittagong, Bangladesh. We have a on going reference based genome assembly and annotation project. We have just received Total file size of 310.2 GB of FASTQ files. I have read in some publication and they mention 350 Gb of Raw data. i am confused is it giga base of giga byte?? i know 1 Gbp (giga base pairs) = 1,000,000,000 bp we have total sequence :199893331 sequence length :40-100 in one part of a FASTQ file should i convert it into Gbp? how can i calculate genome coverage?

coverage assembly gb • 250 views
ADD COMMENTlink written 12 weeks ago by Shawrob4000
gravatar for genomax
12 weeks ago by
United States
genomax58k wrote:

If you have a 100,000,000 bp genome and received 1,000,000,000 bp of sequence data (as a file of reads of equal or variable length) then you have 10x the number of total bases expected to be present in a single copy of the genome.

You can't claim/conclude to have 10x genome coverage since the distribution of reads is never going to be uniform (unless you pre-selected the reads to be so). In places it may be 0 (i.e. no coverage) while in other locations it could be 100x. You would not be able to determine this distribution until you align the reads to the reference (if you have one).

A gigabyte/gibibyte happens to be a measurement of data size in computer science. Depending on type and level of compression a gigabase of sequence will have variable file sizes (measured in some multiple by bytes, of which gigabyte happens to be one measure).

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by genomax58k

thank you very much

ADD REPLYlink written 12 weeks ago by Shawrob4000

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

ADD REPLYlink written 12 weeks ago by WouterDeCoster33k
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