Hi, all,
I have 100 bp pe reads from Hiseq for target genes with size around 200bp. I tried abyss to de novo assemble them.
I used k=40, n=10. When I compared the contigs and the reference sequence, which I used as positive control, I found that there were many small contigs overlapping each other by more than 50bp. Why abyss didn't assemble them into a longer contig? After I increase the k to 60, I saw longer contigs, but there were still overlapping but separate contigs. I am naive to the de bruijn graph and have no ideas about how abyss works. What can I do to get longer contigs instead of shot overlapping ones. Should I increase k more or change the n parameter.
Another question, when I used k=60, did I excluded all reads that are shorter than 60 bp from analysis?
Thanks in advance for your help.
I have 100 bp pe reads from Hiseq for target genes with size around 200bp. I tried abyss to de novo assemble them.
I used k=40, n=10. When I compared the contigs and the reference sequence, which I used as positive control, I found that there were many small contigs overlapping each other by more than 50bp. Why abyss didn't assemble them into a longer contig? After I increase the k to 60, I saw longer contigs, but there were still overlapping but separate contigs. I am naive to the de bruijn graph and have no ideas about how abyss works. What can I do to get longer contigs instead of shot overlapping ones. Should I increase k more or change the n parameter.
Another question, when I used k=60, did I excluded all reads that are shorter than 60 bp from analysis?
Thanks in advance for your help.
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