Hi!
Currently I have a bunch of short read data from different illumina libraries (paired-end, mate pair, single-end) of a bacterial genome. I de novo assembled the read data using different assembly tools and now I want to map the calculated contigs back to a more or less closely related reference genome using bowtie2.
Now I thought that it is possible, to map reads (or in my case contigs) partial to the reference, so for example:
ref:
AAAAAAAAAAGGGGGGGGGGTTTTTTTTTTT
contig:
GGGGGGGGGGXXXXXXXXXX
mapped:
AAAAAAAAAAGGGGGGGGGGTTTTTTTTTTT
-------------GGGGGGGGGG
unmapped:
XXXXXXXXXX
But at the moment, bowtie2 wont map the entire contig and moved it to unmapped.
Did I mis a parameter option or is this scenario not possible with bowtie2?
Thanks!
Martin
Currently I have a bunch of short read data from different illumina libraries (paired-end, mate pair, single-end) of a bacterial genome. I de novo assembled the read data using different assembly tools and now I want to map the calculated contigs back to a more or less closely related reference genome using bowtie2.
Now I thought that it is possible, to map reads (or in my case contigs) partial to the reference, so for example:
ref:
AAAAAAAAAAGGGGGGGGGGTTTTTTTTTTT
contig:
GGGGGGGGGGXXXXXXXXXX
mapped:
AAAAAAAAAAGGGGGGGGGGTTTTTTTTTTT
-------------GGGGGGGGGG
unmapped:
XXXXXXXXXX
But at the moment, bowtie2 wont map the entire contig and moved it to unmapped.
Did I mis a parameter option or is this scenario not possible with bowtie2?
Thanks!
Martin
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