Dear all,
I have paired end as well as mate paired data for de novo assembly. The data size of paired end data is around 91 GB and around 100GB for mate paired data. The read length is 101 nt for paired end data.
The query is, when I trying to estimate genome size using only paired end data with jellyfish as well as BBMAP, the peak was not coming with both the tools. With both above mentioned tools, after initial high values there is no second prominent (ideally) peak. I did cross-check with FastQC results where I got "Sequence Per base" and "GC content" tests failed. Does that mean I don't have good quality of base calling? There are no other tests which are failed than those two, no adapter contamination either.
Can anyone tell me from existing information if I can calculate genome size or data quality is so poor that I can't calculate genome size? I did go through this link http://seqanswers.com/forums/showthread.php?t=41874, but couldn't corelate and conclude properly with my data.
I have paired end as well as mate paired data for de novo assembly. The data size of paired end data is around 91 GB and around 100GB for mate paired data. The read length is 101 nt for paired end data.
The query is, when I trying to estimate genome size using only paired end data with jellyfish as well as BBMAP, the peak was not coming with both the tools. With both above mentioned tools, after initial high values there is no second prominent (ideally) peak. I did cross-check with FastQC results where I got "Sequence Per base" and "GC content" tests failed. Does that mean I don't have good quality of base calling? There are no other tests which are failed than those two, no adapter contamination either.
Can anyone tell me from existing information if I can calculate genome size or data quality is so poor that I can't calculate genome size? I did go through this link http://seqanswers.com/forums/showthread.php?t=41874, but couldn't corelate and conclude properly with my data.
Comment