Question: Bowtie2 mapping of (several, long) contigs in fasta to a reference sequence - contig sequences only mapped as 60 bp
0
gravatar for kalfsnes
2.3 years ago by
kalfsnes10
kalfsnes10 wrote:

I've got contigs from de novo (Spades) assembly (approx 175 contigs of length 200 bp to 11 kb), and want to map these to a reference sequence and make a new consensus. I have tried using Bowtie2 and I do get an output. However, all the aligned contigs have been truncated down to 60 bp.

I've tried changing the Bowtie2 index to "large index", Bowtie2 is run using the -f and -U options.

Any help appreciated.

ADD COMMENTlink written 2.3 years ago by kalfsnes10
3
gravatar for Devon Ryan
2.3 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:
  1. Does your fasta file have 60 base wide lines?
  2. You don't need a large index.
  3. I would strongly recommend that you use bwa (or minimap2) instead. It's unclear how good bowtie2 will be with long contigs.
ADD COMMENTlink written 2.3 years ago by Devon Ryan92k
  1. Yes, but shouldn't Bowtie2 handle these line breaks? Anyway, I removed them, but that left me with a new problem - memory. I'll try run it on computer with more memory, see if that solves it.
  2. Okay.
  3. Worked like a charm with bwa - thanks! :-)
ADD REPLYlink written 2.3 years ago by kalfsnes10
1

Nah, it expects sequences on a single line for fastq files, so fasta will be the same. I expect most aligners that accept fasta input are like that.

ADD REPLYlink written 2.3 years ago by Devon Ryan92k
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