Hello Everybody. How does one calculate the coverage on a paired end Illumina GA II X run? My fast qc statistics for the reads are as follows:
Foward reads: 1,95,71,148. No of Bases: 1,05,68,41,992 file size: 3.9 GB
Reverse reads: 1,95,71,148 No of Bases: 1,05,68,41,992 3.9 GB
This is a mouse genome we have sequenced. The size of the mouse genome in bases is: 2,7,1,69,65,481 which corresponds to 2.5 GB.
Do i follow the simple calculation of C = LN / G
• C stands for coverage
• G is the haploid genome length
• L is the read length
• N is the number of reads
Doing this results in a measly 0.77 X coverage which is too low , in which case it is unacceptable for the experiment. am i calculating this correctly?
I cannot map my reads to a reference mouse genome to use coveragebed or any other function/tool, because of the nature of my experiment which wont allow a large no. of reads to map. So finding the uniquely mapped reads is out of question. I also cannot do a de novo assembly because of computer memory constraints. Any thoughts on this are appreciated. Thanks in advance!
Foward reads: 1,95,71,148. No of Bases: 1,05,68,41,992 file size: 3.9 GB
Reverse reads: 1,95,71,148 No of Bases: 1,05,68,41,992 3.9 GB
This is a mouse genome we have sequenced. The size of the mouse genome in bases is: 2,7,1,69,65,481 which corresponds to 2.5 GB.
Do i follow the simple calculation of C = LN / G
• C stands for coverage
• G is the haploid genome length
• L is the read length
• N is the number of reads
Doing this results in a measly 0.77 X coverage which is too low , in which case it is unacceptable for the experiment. am i calculating this correctly?
I cannot map my reads to a reference mouse genome to use coveragebed or any other function/tool, because of the nature of my experiment which wont allow a large no. of reads to map. So finding the uniquely mapped reads is out of question. I also cannot do a de novo assembly because of computer memory constraints. Any thoughts on this are appreciated. Thanks in advance!
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