Question: Mapping contigs & scaffolds to ref genome?
0
gravatar for YOUSEUFS
3.3 years ago by
YOUSEUFS20
YOUSEUFS20 wrote:

Noob here,

I'm trying to map a file of contigs and scaffolds onto a reference genome but bowtie keeps outputting the same error:

bowtie2 -f -x wmel_genome -U ~/Aa23/ref/assemblies/wMelPopPGYP.finalassembly-alt.fasta

terminate called after throwing an instance of 'std::bad_alloc'

what(): std::bad_alloc

(ERR): bowtie2-align died with signal 6 (ABRT)

I edited my file from a non-fasta so that every contig/scaffold sequence began with ">scaffold/contig-name". There are over 15 separated sequences in the file. Some of the sequences contain "n" character I'm guessing for uncertain/missing nucleotides.

bowtie2 mapping assembly • 3.1k views
ADD COMMENTlink modified 2.5 years ago by h.mon32k • written 3.3 years ago by YOUSEUFS20
3
gravatar for Sej Modha
3.3 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

Bowtie2 is a short read mapper and is not suitable for such application, BLAT or MUMMER would be more suitable in such cases.

ADD COMMENTlink written 3.3 years ago by Sej Modha4.7k
3
gravatar for colindaven
3.3 years ago by
colindaven2.6k
Hannover Medical School
colindaven2.6k wrote:

I find bwa mem is useful for this case and have used it many times. Bowtie2 is not suitable.

I would use samtools, not picard, for the SAM-> bam conversion, as Picard gets messed up by very long MD strings from long contigs

ADD COMMENTlink written 3.3 years ago by colindaven2.6k
1
gravatar for cschu181
2.7 years ago by
cschu1812.5k
cschu1812.5k wrote:

You can also try gmap, I find that works quite well.

ADD COMMENTlink written 2.7 years ago by cschu1812.5k
1
gravatar for WouterDeCoster
2.7 years ago by
Belgium
WouterDeCoster45k wrote:

Minimap2 should also be able to do this job.

ADD COMMENTlink written 2.7 years ago by WouterDeCoster45k
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