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Forum: Bioinformatics 05-19-2017, 07:21 PM
Replies: 10
Views: 524
Posted By wb1016
Soapdenovo2 was the assembler since i have...

Soapdenovo2 was the assembler

since i have no reference to align ,so the coverage remains unclear
Forum: Bioinformatics 05-19-2017, 06:55 AM
Replies: 10
Views: 524
Posted By wb1016
I invested a lot of money to build seven genome...

I invested a lot of money to build seven genome libraries (including very large ones) for the project, it is expected to be a de novo sequencing... really upset with this problem...
Forum: Bioinformatics 05-19-2017, 06:26 AM
Replies: 10
Views: 524
Posted By wb1016
That's true. The GC content of the bird genome is...

That's true. The GC content of the bird genome is always biased.

The only thing is the poly kmers, don't know if this was a problematic sequencing and it caused the failure of the assembly..
Forum: Bioinformatics 05-19-2017, 05:59 AM
Replies: 10
Views: 524
Posted By wb1016
The Per base sequence content also seems...

The Per base sequence content also seems problematic, and other plots are fine, especially the Sequence Quality is very good.

Have trimmed the adapters and the low-quality reads before assembly.
Forum: Bioinformatics 05-19-2017, 05:36 AM
Replies: 10
Views: 524
Posted By wb1016
FastQC Kmer, polyA, polyG, polyC, polyT...

Hi all,

I got the Illumina reads from a NGS company. It is a bird genome. The quality control running by fastQC seems very weird. Too many poly kmers as attached.

Also, I have run the assembly,...
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